551
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Alcendor DJ, Matthews-Juarez P, Smoot D, Hildreth JEK, Lamar K, Tabatabai M, Wilus D, Juarez PD. Breakthrough COVID-19 Infections in the US: Implications for Prolonging the Pandemic. Vaccines (Basel) 2022; 10:755. [PMID: 35632512 PMCID: PMC9146933 DOI: 10.3390/vaccines10050755] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/27/2022] [Accepted: 05/06/2022] [Indexed: 02/04/2023] Open
Abstract
The incidence of COVID-19 breakthrough infections-an infection that occurs after you have been vaccinated-has increased in frequency since the Delta and now Omicron variants of the SARS-CoV-2 coronavirus have become the dominant strains transmitted in the United States (US). Evidence suggests that individuals with breakthrough infections, though rare and expected, may readily transmit COVID-19 to unvaccinated populations, posing a continuing threat to the unvaccinated. Here, we examine factors contributing to breakthrough infections including a poor immune response to the vaccines due to the fact of advanced age and underlying comorbidities, the natural waning of immune protection from the vaccines over time, and viral variants that escape existing immune protection from the vaccines. The rise in breakthrough infections in the US and how they contribute to new infections, specifically among the unvaccinated and individuals with compromised immune systems, will create the need for additional booster vaccinations or development of modified vaccines that directly target current variants circulating among the general population. The need to expedite vaccination among the more than 49.8 million unvaccinated eligible people in the US is critical.
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Affiliation(s)
- Donald J. Alcendor
- Department of Microbiology, Immunology and Physiology, Center for AIDS Health Disparities Research, School of Medicine, Meharry Medical College, 1005 D.B. Todd Jr. Blvd., Nashville, TN 37208, USA;
- Center for AIDS Health Disparities Research, Department of Microbiology, Immunology, and Physiology, School of Medicine, Meharry Medical College, 1005 D.B. Todd Jr. Blvd., Hubbard Hospital, 5th Floor, Rm. 5025, Nashville, TN 37208, USA
| | - Patricia Matthews-Juarez
- Department of Family & Community Medicine, Meharry Medical College, 1005 D.B. Todd Jr. Blvd., Nashville, TN 37208, USA; (P.M.-J.); (P.D.J.)
| | - Duane Smoot
- Department of Internal Medicine, School of Medicine, Meharry Medical College, 1005 D.B. Todd Jr. Blvd., Nashville, TN 37208, USA;
| | - James E. K. Hildreth
- Department of Microbiology, Immunology and Physiology, Center for AIDS Health Disparities Research, School of Medicine, Meharry Medical College, 1005 D.B. Todd Jr. Blvd., Nashville, TN 37208, USA;
- Center for AIDS Health Disparities Research, Department of Microbiology, Immunology, and Physiology, School of Medicine, Meharry Medical College, 1005 D.B. Todd Jr. Blvd., Hubbard Hospital, 5th Floor, Rm. 5025, Nashville, TN 37208, USA
- Department of Internal Medicine, School of Medicine, Meharry Medical College, 1005 D.B. Todd Jr. Blvd., Nashville, TN 37208, USA;
| | - Kimberly Lamar
- Office of Health Disparities Elimination, Tennessee Department of Health, Nashville, TN 37243, USA;
| | - Mohammad Tabatabai
- School of Graduate Studies and Research, Meharry Medical College, 1005 D.B. Todd Jr. Blvd., Nashville, TN 37208, USA; (M.T.); (D.W.)
| | - Derek Wilus
- School of Graduate Studies and Research, Meharry Medical College, 1005 D.B. Todd Jr. Blvd., Nashville, TN 37208, USA; (M.T.); (D.W.)
| | - Paul D. Juarez
- Department of Family & Community Medicine, Meharry Medical College, 1005 D.B. Todd Jr. Blvd., Nashville, TN 37208, USA; (P.M.-J.); (P.D.J.)
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552
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Abstract
Immunocompromised hosts with prolonged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections have been implicated in the emergence of highly mutated SARS-CoV-2 variants. Spike mutations are of particular concern because the spike protein is a key target for vaccines and therapeutics for SARS-CoV-2. Here, we report the emergence of spike mutations in two immunocompromised patients with persistent SARS-CoV-2 reverse transcription (RT)-PCR positivity (>90 days). Whole-genome sequence analysis of samples obtained before and after coronavirus disease 2019 (COVID-19) treatment demonstrated the development of partial therapeutic escape mutations and increased intrahost SARS-CoV-2 genome diversity over time. This case series thus adds to the accumulating evidence that immunocompromised hosts with persistent infections are important sources of SARS-CoV-2 genome diversity and, in particular, clinically important spike protein diversity. IMPORTANCE The emergence of clinically important mutations described in this report highlights the need for sustained vigilance and containment measures when managing immunocompromised patients with persistent COVID-19. Even as jurisdictions across the globe start lifting pandemic control measures, immunocompromised patients with persistent COVID-19 constitute a unique group that requires close genomic monitoring and enhanced infection control measures, to ensure early detection and containment of mutations and variants of therapeutic and public health importance.
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553
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Sette A, Saphire EO. Inducing broad-based immunity against viruses with pandemic potential. Immunity 2022; 55:738-748. [PMID: 35545026 DOI: 10.1016/j.immuni.2022.04.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/06/2022] [Accepted: 04/13/2022] [Indexed: 02/08/2023]
Abstract
The brutal toll of another viral pandemic can be blunted by investing now in research that uncovers mechanisms of broad-based immunity so we may have vaccines and therapeutics at the ready. We do not know exactly what pathogen may trigger the next wave or next pandemic. We do know, however, that the human immune system must respond and must be bolstered with effective vaccines and other therapeutics to preserve lives and livelihoods. These countermeasures must focus on features conserved among families of pathogens in order to be responsive against something yet to emerge. Here, we focus on immunological approaches to mitigate the impact of the next emerging virus pandemic by developing vaccines that elicit both broadly protective antibodies and T cells. Identifying human immune mechanisms of broad protection against virus families with pandemic potential will be our best defense for humanity in the future.
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Affiliation(s)
- Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA.
| | - Erica Ollmann Saphire
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA.
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554
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Sonnleitner ST, Prelog M, Sonnleitner S, Hinterbichler E, Halbfurter H, Kopecky DBC, Almanzar G, Koblmüller S, Sturmbauer C, Feist L, Horres R, Posch W, Walder G. Cumulative SARS-CoV-2 mutations and corresponding changes in immunity in an immunocompromised patient indicate viral evolution within the host. Nat Commun 2022; 13:2560. [PMID: 35538074 PMCID: PMC9090742 DOI: 10.1038/s41467-022-30163-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 04/19/2022] [Indexed: 01/07/2023] Open
Abstract
Different scenarios explaining the emergence of novel variants of concern (VOC) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been reported, including their evolution in scarcely monitored populations, in animals as alternative hosts, or in immunocompromised individuals. Here we report SARS-CoV-2 immune escape mutations over a period of seven months in an immunocompromised patient with prolonged viral shedding. Signs of infection, viral shedding and mutation events are periodically analyzed using RT-PCR and next-generation sequencing based on naso-pharyngeal swabs, with the results complemented by immunological diagnostics to determine humoral and T cell immune responses. Throughout the infection course, 17 non-synonymous intra-host mutations are noted, with 15 (88.2%) having been previously described as prominent immune escape mutations (S:E484K, S:D950N, S:P681H, S:N501Y, S:del(9), N:S235F and S:H655Y) in VOCs. The high frequency of these non-synonymous mutations is consistent with multiple events of convergent evolution. Thus, our results suggest that specific mutations in the SARS-CoV-2 genome may represent positions with a fitness advantage, and may serve as targets in future vaccine and therapeutics development for COVID-19. Variants of concerns arise from SARS-CoV-2 mutations poise as severe public health threats. Here the authors chronicle SARS-CoV-2 mutations onset and immune parameters in an immunocompromised patient with continuous virus-shedding, thereby hinting potential intra-host viral evolution and escape facilitated by ineffective T cell immunity.
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Affiliation(s)
- Sissy Therese Sonnleitner
- Infektiologie Tirol, Department of Virology, 9931, Unterwalden 30, Außervillgraten, Austria. .,Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, 6020, Innsbruck, Austria.
| | - Martina Prelog
- Pediatric Rheumatology/Special Immunology, Department of Pediatrics, University Hospital Wuerzburg, Josef-Schneider-Str. 2, Wuerzburg, Germany
| | - Stefanie Sonnleitner
- Infektiologie Tirol, Department of Virology, 9931, Unterwalden 30, Außervillgraten, Austria
| | - Eva Hinterbichler
- Infektiologie Tirol, Department of Virology, 9931, Unterwalden 30, Außervillgraten, Austria
| | - Hannah Halbfurter
- Infektiologie Tirol, Department of Virology, 9931, Unterwalden 30, Außervillgraten, Austria
| | - Dominik B C Kopecky
- Infektiologie Tirol, Department of Virology, 9931, Unterwalden 30, Außervillgraten, Austria
| | - Giovanni Almanzar
- Pediatric Rheumatology/Special Immunology, Department of Pediatrics, University Hospital Wuerzburg, Josef-Schneider-Str. 2, Wuerzburg, Germany
| | - Stephan Koblmüller
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria
| | - Christian Sturmbauer
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria
| | - Leonard Feist
- GenXPro GmbH, Altenhoeferallee 3, 60438, Frankfurt am Main, Germany
| | - Ralf Horres
- GenXPro GmbH, Altenhoeferallee 3, 60438, Frankfurt am Main, Germany
| | - Wilfried Posch
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Gernot Walder
- Infektiologie Tirol, Department of Virology, 9931, Unterwalden 30, Außervillgraten, Austria
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555
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Windsor IW, Tong P, Lavidor O, Sanjari Moghaddam A, McKay LGA, Gautam A, Chen Y, MacDonald EA, Yoo DK, Griffiths A, Wesemann DR, Harrison SC. Antibodies induced by ancestral SARS-CoV-2 strain that cross-neutralize variants from Alpha to Omicron BA.1. Sci Immunol 2022; 7:eabo3425. [PMID: 35536154 PMCID: PMC9097876 DOI: 10.1126/sciimmunol.abo3425] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Neutralizing antibodies that recognize the SARS-CoV-2 spike glycoprotein are the principal host defense against viral invasion. Variants of SARS-CoV-2 bear mutations that allow escape from neutralization by many antibodies, especially those belonging to classes widely distributed in the human population. Identifying antibodies that neutralize these variants of concern and determining their prevalence are important goals for understanding immune protection. To determine the Delta- and Omicron BA.1-variant specificity of B cell repertoires established by an initial Wuhan strain infection, we measured neutralization potencies of 73 antibodies from an unbiased survey of the early memory B cell response. Antibodies recognizing each of three, previously defined, epitopic regions on the spike receptor-binding domain (RBD) varied in neutralization potency and variant-escape resistance. The ACE2 binding surface (“RBD-2”) harbored the binding sites of the neutralizing antibodies with highest potency but with the greatest sensitivity to viral escape; two other epitopic regions on the RBD (“RBD-1 and “RBD-3”) bound antibodies of more modest potency but greater breadth. The structures of several Fab:spike complexes that neutralized all five variants of concern tested, including one Fab each from the RBD-1, -2 and -3 clusters, illustrated the determinants of broad neutralization and showed that B cell repertoires can have specificities that avoid immune escape driven by widely distributed (“public”) antibodies. The structure of the RBD-2-binding, broad neutralizer shows why it retains neutralizing activity for Omicron BA.1, unlike most others in the same public class. Our results correlate with real-world data on vaccine efficacy, which indicate mitigation of disease caused by Omicron BA.1.
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Affiliation(s)
- Ian W Windsor
- Boston Children's Hospital, Boston, MA 02115, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.,Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Pei Tong
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA.,Department of Medicine, Division of Allergy and Clinical Immunology, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Olivia Lavidor
- Boston Children's Hospital, Boston, MA 02115, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Ali Sanjari Moghaddam
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA.,Department of Medicine, Division of Allergy and Clinical Immunology, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Lindsay G A McKay
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02115.,National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02115
| | - Avneesh Gautam
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA.,Department of Medicine, Division of Allergy and Clinical Immunology, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Yuezhou Chen
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA.,Department of Medicine, Division of Allergy and Clinical Immunology, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Elizabeth A MacDonald
- Boston Children's Hospital, Boston, MA 02115, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Duck Kyun Yoo
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA.,Department of Medicine, Division of Allergy and Clinical Immunology, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Anthony Griffiths
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02115.,National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02115.,Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA
| | - Duane R Wesemann
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA.,Department of Medicine, Division of Allergy and Clinical Immunology, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.,Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA
| | - Stephen C Harrison
- Boston Children's Hospital, Boston, MA 02115, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Boston, MA 02115, USA
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556
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Adams CD, Tielbeek JJ, Boutwell BB. Shared genomic architectures of COVID-19 and antisocial behavior. Transl Psychiatry 2022; 12:193. [PMID: 35538069 PMCID: PMC9086665 DOI: 10.1038/s41398-022-01948-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 04/16/2022] [Accepted: 04/21/2022] [Indexed: 11/11/2022] Open
Abstract
Little is known about the genetics of norm violation and aggression in relation to coronavirus disease 2019 (COVID-19). To investigate this, we used summary statistics from genome-wide association studies and linkage disequilibrium score regression to calculate a matrix of genetic correlations (rgs) for antisocial behavior (ASB), COVID-19, and various health and behavioral traits. After false-discovery rate correction, ASB was genetically correlated with COVID-19 (rg = 0.51; P = 1.54E-02) and 19 other traits. ASB and COVID-19 were both positively genetically correlated with having a noisy workplace, doing heavy manual labor, chronic obstructive pulmonary disease, and genitourinary diseases. ASB and COVID-19 were both inversely genetically correlated with average income, education years, healthspan, verbal reasoning, lifespan, cheese intake, and being breastfed as a baby. But keep in mind that rgs are not necessarily causal. And, if causal, their prevailing directions of effect (which causes which) are indiscernible from rgs alone. Moreover, the SNP-heritability ([Formula: see text]) estimates for two measures of COVID-19 were very small, restricting the overlap of genetic variance in absolute terms between ASB and COVID-19. Nonetheless, our findings suggest that those with antisocial tendencies possibly have a higher risk of exposure to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) than those without antisocial tendencies. This may have been especially true early in the pandemic before vaccines against SARS-CoV-2 were available and before the emergence of the highly transmissible Omicron variant.
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Affiliation(s)
- Charleen D. Adams
- grid.38142.3c000000041936754XDepartment of Environmental Health, Program in Molecular and Integrative Physiological Sciences, Harvard T.H. Chan School of Public Health, Boston, MA USA
| | - Jorim J. Tielbeek
- grid.12380.380000 0004 1754 9227Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Brian B. Boutwell
- grid.251313.70000 0001 2169 2489School of Applied Sciences, The University of Mississippi, University, MO USA ,grid.410721.10000 0004 1937 0407John D. Bower School of Population Health, University of Mississippi Medical Center, Jackson, MI USA
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557
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Increased Receptor Affinity and Reduced Recognition by Specific Antibodies Contribute to Immune Escape of SARS-CoV-2 Variant Omicron. Vaccines (Basel) 2022; 10:vaccines10050743. [PMID: 35632499 PMCID: PMC9147318 DOI: 10.3390/vaccines10050743] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 02/04/2023] Open
Abstract
In this report, we mechanistically reveal how the Variant of Concern (VOC) SARS-CoV-2 Omicron (B.1.1.529) escapes neutralizing antibody responses, by physio-chemical characterization of this variant in comparison to the wild-type Wuhan and the Delta variant (B.1.617.2). Convalescent sera, as well as sera obtained from participants who received two or three doses of mRNA vaccines (Moderna-mRNA-1273® or Pfizer-BNT162b2®), were used for comparison in this study. Our data demonstrate that both Delta, as well as Omicron variants, exhibit a higher affinity for the receptor ACE2, facilitating infection and causing antibody escape by receptor affinity (affinity escape), due to the reduced ability of antibodies to compete with RBD-receptor interaction and virus neutralization. In contrast, only Omicron but not the Delta variant escaped antibody recognition, most likely because only Omicron exhibits the mutation at E484A, a position associated with reduced recognition, resulting in further reduced neutralization (specificity escape). Nevertheless, the immunizations with RNA-based vaccines resulted in marked viral neutralization in vitro for all strains, compatible with the fact that Omicron is still largely susceptible to vaccination-induced antibodies, despite affinity- and specificity escape.
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558
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Jawad B, Adhikari P, Podgornik R, Ching WY. Binding Interactions between Receptor-Binding Domain of Spike Protein and Human Angiotensin Converting Enzyme-2 in Omicron Variant. J Phys Chem Lett 2022; 13:3915-3921. [PMID: 35481766 PMCID: PMC9063111 DOI: 10.1021/acs.jpclett.2c00423] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The emergence of new SARS-CoV-2 Omicron variant of concern (OV) has exacerbated the COVID-19 pandemic because of a large number of mutations in the spike protein, particularly in the receptor-binding domain (RBD), resulting in highly contagious and/or vaccine-resistant strains. Herein, we present a systematic analysis based on detailed molecular dynamics (MD) simulations in order to understand how the OV RBD mutations affect the ACE2 binding. We show that the OV RBD binds to ACE2 more efficiently and tightly predominantly because of strong electrostatic interactions, thereby promoting increased infectivity and transmissibility compared to other strains. Some of the OV RBD mutations are predicted to affect the antibody neutralization either through their role in the S-protein conformational changes, such as S371L, S373P, and S375F, or through changing its surface charge distribution, such as G339D, N440K, T478K, and E484A. Other mutations, such as K417N, G446S, and Y505H, decrease the ACE2 binding, whereas S447N, Q493R, G496S, Q498R, and N501Y tend to increase it.
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Affiliation(s)
- Bahaa Jawad
- Department
of Physics and Astronomy, University of
Missouri—Kansas City, Kansas City, Missouri 64110, United States
- Department
of Applied Sciences, University of Technology, Baghdad 10066, Iraq
| | - Puja Adhikari
- Department
of Physics and Astronomy, University of
Missouri—Kansas City, Kansas City, Missouri 64110, United States
| | - Rudolf Podgornik
- Wenzhou
Institute of the University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
- School
of Physical Sciences and Kavli Institute of Theoretical Science, University of Chinese Academy of Sciences, Beijing 100049, China
- CAS
Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100090, China
- Department
of Physics, Faculty of Mathematics and Physics, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Wai-Yim Ching
- Department
of Physics and Astronomy, University of
Missouri—Kansas City, Kansas City, Missouri 64110, United States
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559
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Guo H, Gao Y, Li T, Li T, Lu Y, Zheng L, Liu Y, Yang T, Luo F, Song S, Wang W, Yang X, Nguyen HC, Zhang H, Huang A, Jin A, Yang H, Rao Z, Ji X. Structures of Omicron spike complexes and implications for neutralizing antibody development. Cell Rep 2022; 39:110770. [PMID: 35477022 PMCID: PMC9010281 DOI: 10.1016/j.celrep.2022.110770] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/16/2022] [Accepted: 04/11/2022] [Indexed: 01/18/2023] Open
Abstract
The emergence of the SARS-CoV-2 Omicron variant is dominant in many countries worldwide. The high number of spike mutations is responsible for the broad immune evasion from existing vaccines and antibody drugs. To understand this, we first present the cryo-electron microscopy structure of ACE2-bound SARS-CoV-2 Omicron spike. Comparison to previous spike antibody structures explains how Omicron escapes these therapeutics. Secondly, we report structures of Omicron, Delta, and wild-type spikes bound to a patient-derived Fab antibody fragment (510A5), which provides direct evidence where antibody binding is greatly attenuated by the Omicron mutations, freeing spike to bind ACE2. Together with biochemical binding and 510A5 neutralization assays, our work establishes principles of binding required for neutralization and clearly illustrates how the mutations lead to antibody evasion yet retain strong ACE2 interactions. Structural information on spike with both bound and unbound antibodies collectively elucidates potential strategies for generation of therapeutic antibodies.
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Affiliation(s)
- Hangtian Guo
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Institute of Viruses and Infectious Diseases, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University, Nanjing, China,Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yan Gao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China,Shanghai Clinical Research and Trial Center, 201210 Shanghai, P.R. China
| | - Tinghan Li
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Institute of Viruses and Infectious Diseases, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University, Nanjing, China
| | - Tingting Li
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing 400010, China,Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing 400010, China
| | - Yuchi Lu
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Le Zheng
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Institute of Viruses and Infectious Diseases, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University, Nanjing, China
| | - Yue Liu
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Institute of Viruses and Infectious Diseases, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University, Nanjing, China
| | - Tingting Yang
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Institute of Viruses and Infectious Diseases, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University, Nanjing, China
| | - Feiyang Luo
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing 400010, China,Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing 400010, China
| | - Shuyi Song
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing 400010, China,Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing 400010, China
| | - Wei Wang
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400010, China
| | - Xiuna Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China,Shanghai Clinical Research and Trial Center, 201210 Shanghai, P.R. China
| | - Henry C. Nguyen
- Asher Biotherapeutics, 650 Gateway Blvd, Suite 100, South San Francisco, CA 94080, USA
| | - Hongkai Zhang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China,State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300350, P.R. China
| | - Ailong Huang
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing 400010, China,Corresponding author
| | - Aishun Jin
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing 400010, China,Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing 400010, China,Corresponding author
| | - Haitao Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China,Shanghai Clinical Research and Trial Center, 201210 Shanghai, P.R. China,Corresponding author
| | - Zihe Rao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China,Laboratory of Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, China,Corresponding author
| | - Xiaoyun Ji
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Institute of Viruses and Infectious Diseases, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University, Nanjing, China,Institute of Life Sciences, Chongqing Medical University, Chongqing 400010, China,Engineering Research Center of Protein and Peptide Medicine, Ministry of Education, Nanjing, China,Corresponding author
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560
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Li M, Wang H, Tian L, Pang Z, Yang Q, Huang T, Fan J, Song L, Tong Y, Fan H. COVID-19 vaccine development: milestones, lessons and prospects. Signal Transduct Target Ther 2022; 7:146. [PMID: 35504917 PMCID: PMC9062866 DOI: 10.1038/s41392-022-00996-y] [Citation(s) in RCA: 156] [Impact Index Per Article: 78.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 04/11/2022] [Accepted: 04/13/2022] [Indexed: 12/15/2022] Open
Abstract
With the constantly mutating of SARS-CoV-2 and the emergence of Variants of Concern (VOC), the implementation of vaccination is critically important. Existing SARS-CoV-2 vaccines mainly include inactivated, live attenuated, viral vector, protein subunit, RNA, DNA, and virus-like particle (VLP) vaccines. Viral vector vaccines, protein subunit vaccines, and mRNA vaccines may induce additional cellular or humoral immune regulations, including Th cell responses and germinal center responses, and form relevant memory cells, greatly improving their efficiency. However, some viral vector or mRNA vaccines may be associated with complications like thrombocytopenia and myocarditis, raising concerns about the safety of these COVID-19 vaccines. Here, we systemically assess the safety and efficacy of COVID-19 vaccines, including the possible complications and different effects on pregnant women, the elderly, people with immune diseases and acquired immunodeficiency syndrome (AIDS), transplant recipients, and cancer patients. Based on the current analysis, governments and relevant agencies are recommended to continue to advance the vaccine immunization process. Simultaneously, special attention should be paid to the health status of the vaccines, timely treatment of complications, vaccine development, and ensuring the lives and health of patients. In addition, available measures such as mix-and-match vaccination, developing new vaccines like nanoparticle vaccines, and optimizing immune adjuvant to improve vaccine safety and efficacy could be considered.
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Affiliation(s)
- Maochen Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Han Wang
- Laboratory for Clinical Immunology, Harbin Children's Hospital, Harbin, China
| | - Lili Tian
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Zehan Pang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Qingkun Yang
- College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, China
| | - Tianqi Huang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Junfen Fan
- Institute of Cerebrovascular Disease Research and Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Lihua Song
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China.
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China. .,Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, China.
| | - Huahao Fan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China.
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Rodriguez-Sevilla JJ, Güerri-Fernádez R, Bertran Recasens B. Is There Less Alteration of Smell Sensation in Patients With Omicron SARS-CoV-2 Variant Infection? Front Med (Lausanne) 2022; 9:852998. [PMID: 35492353 PMCID: PMC9039252 DOI: 10.3389/fmed.2022.852998] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/23/2022] [Indexed: 01/05/2023] Open
Abstract
The ongoing pandemic Coronavirus Disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a matter of global concern in terms of public health Within the symptoms secondary to SARS-CoV-2 infection, hyposmia and anosmia have emerged as characteristic symptoms during the onset of the pandemic. Although many researchers have investigated the etiopathogenesis of this phenomenon, the main cause is not clear. The appearance of the new variant of concern Omicron has meant a breakthrough in the chronology of this pandemic, presenting greater transmissibility and less severity, according to the first reports. We have been impressed by the decrease in anosmia reported with this new variant and in patients reinfected or who had received vaccination before becoming infected. Based on the literature published to date, this review proposes different hypotheses to explain this possible lesser affectation of smell. On the one hand, modifications in the SARS-CoV-2 spike protein could produce changes in cell tropism and interaction with proteins that promote virus uptake (ACE-2, TMPRSS2, and TMEM16F). These proteins can be found in the sustentacular cells and glandular cells of the olfactory epithelium. Second, due to the characteristics of the virus or previous immunity (infection or vaccination), there could be less systemic or local inflammation that would generate less cell damage in the olfactory epithelium and/or in the central nervous system.
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Affiliation(s)
| | - Roberto Güerri-Fernádez
- Infectious Diseases Department, Hospital del Mar Institute of Medical Research (IMIM), Barcelona, Spain.,Facultad de Medicina y Ciencias de la Vida (MELIS), Universitat Pompeu Fabra, Barcelona, Spain
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562
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Furukawa K, Tjan LH, Kurahashi Y, Sutandhio S, Nishimura M, Arii J, Mori Y. Assessment of Neutralizing Antibody Response Against SARS-CoV-2 Variants After 2 to 3 Doses of the BNT162b2 mRNA COVID-19 Vaccine. JAMA Netw Open 2022; 5:e2210780. [PMID: 35532938 PMCID: PMC9086840 DOI: 10.1001/jamanetworkopen.2022.10780] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/19/2022] [Indexed: 12/27/2022] Open
Abstract
Importance Although 2 and 3 doses of vaccine have been implemented against the SARS-CoV-2 pandemic, the level of immunity achieved by these additional vaccinations remains unclear. Objective To investigate the induction of neutralizing antibodies against the SARS-CoV-2 Omicron variant after 2 and 3 doses of the BNT162b2 messenger RNA (mRNA) vaccine among recipients of different ages. Design, Setting, and Participants A cohort study was conducted from June 1, 2021, to January 12, 2022, among 82 physicians at Kobe University Hospital who had received 2 doses of the BNT162b2 mRNA vaccine. Main Outcomes and Measures The rates of positive test results and the titers of neutralizing antibodies against the Omicron variant after 2 and 3 doses of the vaccine were compared with those against other variants and compared among 3 age groups (≤38 years [younger age group], 39-58 years [intermediate age group], and ≥59 years [older age group]). Results A total of 82 physicians (71 men [87%]; median age, 44 years [IQR, 33-58 years]) participated; 31 (38%) were in the younger age group, 32 (39%) were in the intermediate age group, and 19 (23%) were in the older age group. At 2 months after 2 doses of the vaccine, 23 participants (28%) had neutralizing antibodies against the Omicron variant, with a titer of 1.3 (95% CI, 1.2-1.4), which was 11.8-fold (95% CI, 9.9-13.9) lower than the titer against the D614G variant and the lowest among the variants tested. Although the titer of the neutralizing antibody against the Delta variant tended to be low among the older age group (2.9 [95% CI, 2.0-4.1]), the titers of the neutralizing antibody against the Omicron variant were low among all age groups (younger age group, 1.3 [95% CI, 1.1-1.6]; intermediate age group, 1.3 (95% CI, [95% CI, 1.1-1.5]; and older age group, 1.2 [95% CI, 1.0-1.4]). At 7 months after 2 doses of the vaccine, 5 participants (6%) had the neutralizing antibody against the Omicron variant, but after the booster (third dose) vaccination, all 72 participants who received the booster had the neutralizing antibody, and the titer was 41 (95% CI, 34-49), much higher than that at 7 months after 2 doses of the vaccine (1.0 [95% CI, 1.0-1.1]). This increase in titers was observed regardless of age groups; the titers were 44 (95% CI, 32-59) among the younger age group, 44 (95% CI, 32-59) among the intermediate age group, and 30 (95% CI, 22-41) among the older age group. Conclusions and Relevance In this cohort study of 82 Japanese participants, 2 doses of the BNT162b2 mRNA vaccine did not induce sufficient neutralizing antibody against the Omicron variant. However, booster vaccination was associated with induction of a high level of neutralizing antibodies against the Omicron variant, irrespective of the recipient's age.
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Affiliation(s)
- Koichi Furukawa
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Lidya Handayani Tjan
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Yukiya Kurahashi
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Silvia Sutandhio
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Mitsuhiro Nishimura
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Jun Arii
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Yasuko Mori
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Japan
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563
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Gu M, Pan H, Yuan Y, Zhou X, Chen L, Wang X, Fang F, Hu L, Xie Y, Shen C. Sera Metabolomics Characterization of Patients at Different Stages in Wuhan Identifies Critical Biomarkers of COVID-19. Front Cell Infect Microbiol 2022; 12:882661. [PMID: 35586248 PMCID: PMC9108257 DOI: 10.3389/fcimb.2022.882661] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 03/28/2022] [Indexed: 12/15/2022] Open
Abstract
We have witnessed the 2-year-long global rampage of COVID-19 caused by the wide spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, knowledge about biomarkers of the entire COVID-19 process is limited. Identification of the systemic features of COVID-19 will lead to critical biomarkers and therapeutic targets for early intervention and clinical disease course prediction. Here, we performed a comprehensive analysis of clinical measurements and serum metabolomics in 199 patients with different stages of COVID-19. In particular, our study is the first serum metabolomic analysis of critical rehabilitation patients and critical death patients. We found many differential metabolites in the comparison of metabolomic results between ordinary, severe, and critical patients and uninfected patients. Through the metabolomic results of COVID-19 patients in various stages, and critical rehabilitation patients and critical death patients, we identified a series of differential metabolites as biomarkers, a separate queue and precise distinction, and predicted COVID-19 verification. These differentially expressed metabolites, included 1,2-di-(9Z,12Z-octadecadienoyl)-sn-glycero-3-phosphate, propylparaben, 20-hydroxyeicosatetraenoic acid, triethanolamine, chavicol, disialosyl galactosyl globoside, 1-arachidonoylglycerophosphoinositol, and alpha-methylstyrene, all of which have been identified for the first time as biomarkers in COVID-19 progression. These biomarkers are involved in many pathological and physiological pathways of COVID-19, for example, immune responses, platelet degranulation, and metabolism which might result in pathogenesis. Our results showed valuable information about metabolites obviously altered in COVID-19 patients with different stages, which could shed light on the pathogenesis as well as serve as potential therapeutic agents of COVID-19.
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Affiliation(s)
- Meijia Gu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Huaqin Pan
- Department of Critical Care Medicine, Zhongnan Hospital of Wuhan University; Clinical Research Center of Hubei Critical Care Medicine, Wuhan, China
| | - Yuncong Yuan
- College of Life Sciences, Wuhan University, Wuhan, China
- China Center for Type Culture Collection, Wuhan University, Wuhan, China
| | - Xuemin Zhou
- Shanghai BIOTREE Biological Technology Co., Ltd, Shanghai, China
| | - Luojia Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Xingran Wang
- College of Life Sciences, Wuhan University, Wuhan, China
| | - Fang Fang
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Liu Hu
- College of Life Sciences, Wuhan University, Wuhan, China
| | - Yaxuan Xie
- School of Health Sciences, Wuhan University, Wuhan, China
| | - Chao Shen
- College of Life Sciences, Wuhan University, Wuhan, China
- China Center for Type Culture Collection, Wuhan University, Wuhan, China
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564
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Gudina EK, Ali S, Froeschl G. Omicron: A Blessing in Disguise? Front Public Health 2022; 10:875022. [PMID: 35586013 PMCID: PMC9108174 DOI: 10.3389/fpubh.2022.875022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 04/13/2022] [Indexed: 12/01/2022] Open
Affiliation(s)
- Esayas Kebede Gudina
- Department of Internal Medicine, Jimma University Institute of Health, Jimma, Ethiopia
- *Correspondence: Esayas Kebede Gudina
| | - Solomon Ali
- Department of Microbiology, Immunology and Parasitology, St. Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Guenter Froeschl
- Division of Infectious Diseases and Tropical Medicine, University Hospital, Ludwig-Maximilians-Universität, Munich, Germany
- Center for International Health, Ludwig-Maximilians-Universität, Munich, Germany
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565
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Roessler J, Pich D, Albanese M, Wratil PR, Krähling V, Hellmuth JC, Scherer C, von Bergwelt-Baildon M, Becker S, Keppler OT, Brisson A, Zeidler R, Hammerschmidt W. Quantitation of SARS-CoV-2 neutralizing antibodies with a virus-free, authentic test. PNAS NEXUS 2022; 1:pgac045. [PMID: 36382127 PMCID: PMC9645495 DOI: 10.1093/pnasnexus/pgac045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/02/2022] [Accepted: 04/11/2022] [Indexed: 06/16/2023]
Abstract
Neutralizing antibodies (NAbs), and their concentration in sera of convalescents and vaccinees are a correlate of protection from COVID-19. The antibody concentrations in clinical samples that neutralize SARS-CoV-2 are difficult and very cumbersome to assess with conventional virus neutralization tests (cVNTs), which require work with the infectious virus and biosafety level 3 containment precautions. Alternative virus neutralization tests currently in use are mostly surrogate tests based on direct or competitive enzyme immunoassays or use viral vectors with the spike protein as the single structural component of SARS-CoV-2. To overcome these obstacles, we developed a virus-free, safe and very fast (4.5 h) in vitro diagnostic test based on engineered yet authentic SARS-CoV-2 virus-like-particles (VLPs). They share all features of the original SARS-CoV-2 but lack the viral RNA genome and thus are non-infectious. NAbs induced by infection or vaccination, but also potentially neutralizing monoclonal antibodies can be reliably quantified and assessed with ease and within hours with our test, because they interfere and block the ACE2-mediated uptake of VLPs by recipient cells. Results from the VLP neutralization test (VLPNT) showed excellent specificity and sensitivity and correlated very well with a cVNT using fully infectious SARS-CoV-2. The results also demonstrated the reduced neutralizing capacity of COVID-19 vaccinee sera against variants of concern of SARS-CoV-2 including omicron B.1.1.529, BA.1.
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Affiliation(s)
- Johannes Roessler
- Department of Otorhinolaryngology, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
- Research Unit Gene Vectors, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- German Centre for Infection Research (DZIF), Partner site Munich, Germany
| | - Dagmar Pich
- Research Unit Gene Vectors, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- German Centre for Infection Research (DZIF), Partner site Munich, Germany
| | - Manuel Albanese
- German Centre for Infection Research (DZIF), Partner site Munich, Germany
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Paul R Wratil
- German Centre for Infection Research (DZIF), Partner site Munich, Germany
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Verena Krähling
- Institute of Virology, Faculty of Medicine, Philipps-Universität Marburg, Marburg, Germany
- German Centre for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Marburg, Germany
| | - Johannes C Hellmuth
- Department of Medicine III, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Clemens Scherer
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
- Department of Medicine I, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Michael von Bergwelt-Baildon
- Department of Medicine III, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
- German Cancer Consortium (DKTK), Munich, Germany
| | - Stephan Becker
- Institute of Virology, Faculty of Medicine, Philipps-Universität Marburg, Marburg, Germany
- German Centre for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Marburg, Germany
| | - Oliver T Keppler
- German Centre for Infection Research (DZIF), Partner site Munich, Germany
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Alain Brisson
- UMR-CBMN CNRS-University of Bordeaux-INP, Pessac, France
| | - Reinhard Zeidler
- Department of Otorhinolaryngology, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
- Research Unit Gene Vectors, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- German Centre for Infection Research (DZIF), Partner site Munich, Germany
| | - Wolfgang Hammerschmidt
- Research Unit Gene Vectors, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- German Centre for Infection Research (DZIF), Partner site Munich, Germany
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566
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Improved oral detection is a characteristic of Omicron infection and has implications for clinical sampling and tissue tropism. J Clin Virol 2022; 152:105170. [DOI: 10.1016/j.jcv.2022.105170] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/12/2022] [Accepted: 04/29/2022] [Indexed: 11/18/2022]
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567
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Huang Q, Zeng J, Lang Q, Gao F, Liu D, Tian S, Shi R, Luo L, Wang H, Hu L, Jiang L, Liu Y, Li K, Wu Y, Xu J, Jiang W, Guo N, Chen Z, Hao X, Jin R, Yan J, Sun Y. Impact of various vaccine boosters on neutralization against omicron following prime vaccinations with inactivated or adenovirus-vectored vaccine. Sci Bull (Beijing) 2022; 67:1326-1330. [PMID: 36267300 PMCID: PMC9561939 DOI: 10.1016/j.scib.2022.05.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/23/2022] [Accepted: 04/26/2022] [Indexed: 11/30/2022]
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568
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Gruell H, Vanshylla K, Weber T, Barnes CO, Kreer C, Klein F. Antibody-Mediated Neutralization of SARS-CoV-2. Immunity 2022; 55:925-944. [PMID: 35623355 PMCID: PMC9118976 DOI: 10.1016/j.immuni.2022.05.005] [Citation(s) in RCA: 72] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/06/2022] [Accepted: 05/09/2022] [Indexed: 11/28/2022]
Abstract
Neutralizing antibodies can block infection, clear pathogens, and are essential to provide long-term immunity. Since the onset of the pandemic, SARS-CoV-2 neutralizing antibodies have been comprehensively investigated and critical information on their development, function, and potential use to prevent and treat COVID-19 have been revealed. With the emergence of SARS-CoV-2 immune escape variants, humoral immunity is being challenged, and a detailed understanding of neutralizing antibodies is essential to guide vaccine design strategies as well as antibody-mediated therapies. In this review, we summarize some of the key findings on SARS-CoV-2 neutralizing antibodies, with a focus on their clinical application.
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Affiliation(s)
- Henning Gruell
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Kanika Vanshylla
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Timm Weber
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Christopher O Barnes
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Christoph Kreer
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Florian Klein
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, 50931 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany.
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569
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Strohl WR, Ku Z, An Z, Carroll SF, Keyt BA, Strohl LM. Passive Immunotherapy Against SARS-CoV-2: From Plasma-Based Therapy to Single Potent Antibodies in the Race to Stay Ahead of the Variants. BioDrugs 2022; 36:231-323. [PMID: 35476216 PMCID: PMC9043892 DOI: 10.1007/s40259-022-00529-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2022] [Indexed: 12/15/2022]
Abstract
The COVID-19 pandemic is now approaching 2 years old, with more than 440 million people infected and nearly six million dead worldwide, making it the most significant pandemic since the 1918 influenza pandemic. The severity and significance of SARS-CoV-2 was recognized immediately upon discovery, leading to innumerable companies and institutes designing and generating vaccines and therapeutic antibodies literally as soon as recombinant SARS-CoV-2 spike protein sequence was available. Within months of the pandemic start, several antibodies had been generated, tested, and moved into clinical trials, including Eli Lilly's bamlanivimab and etesevimab, Regeneron's mixture of imdevimab and casirivimab, Vir's sotrovimab, Celltrion's regdanvimab, and Lilly's bebtelovimab. These antibodies all have now received at least Emergency Use Authorizations (EUAs) and some have received full approval in select countries. To date, more than three dozen antibodies or antibody combinations have been forwarded into clinical trials. These antibodies to SARS-CoV-2 all target the receptor-binding domain (RBD), with some blocking the ability of the RBD to bind human ACE2, while others bind core regions of the RBD to modulate spike stability or ability to fuse to host cell membranes. While these antibodies were being discovered and developed, new variants of SARS-CoV-2 have cropped up in real time, altering the antibody landscape on a moving basis. Over the past year, the search has widened to find antibodies capable of neutralizing the wide array of variants that have arisen, including Alpha, Beta, Gamma, Delta, and Omicron. The recent rise and dominance of the Omicron family of variants, including the rather disparate BA.1 and BA.2 variants, demonstrate the need to continue to find new approaches to neutralize the rapidly evolving SARS-CoV-2 virus. This review highlights both convalescent plasma- and polyclonal antibody-based approaches as well as the top approximately 50 antibodies to SARS-CoV-2, their epitopes, their ability to bind to SARS-CoV-2 variants, and how they are delivered. New approaches to antibody constructs, including single domain antibodies, bispecific antibodies, IgA- and IgM-based antibodies, and modified ACE2-Fc fusion proteins, are also described. Finally, antibodies being developed for palliative care of COVID-19 disease, including the ramifications of cytokine release syndrome (CRS) and acute respiratory distress syndrome (ARDS), are described.
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Affiliation(s)
| | - Zhiqiang Ku
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Sciences Center, Houston, TX USA
| | - Zhiqiang An
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Sciences Center, Houston, TX USA
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570
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Guo Y, Han J, Zhang Y, He J, Yu W, Zhang X, Wu J, Zhang S, Kong Y, Guo Y, Lin Y, Zhang J. SARS-CoV-2 Omicron Variant: Epidemiological Features, Biological Characteristics, and Clinical Significance. Front Immunol 2022; 13:877101. [PMID: 35572518 PMCID: PMC9099228 DOI: 10.3389/fimmu.2022.877101] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 04/07/2022] [Indexed: 12/23/2022] Open
Abstract
The SARS-CoV-2 Omicron (B.1.1529) variant was designated as a variant of concern (VOC) by the World Health Organization (WHO) on November 26, 2021. Within two months, it had replaced the Delta variant and had become the dominant circulating variant around the world. The Omicron variant possesses an unprecedented number of mutations, especially in the spike protein, which may be influencing its biological and clinical aspects. Preliminary studies have suggested that increased transmissibility and the reduced protective effects of neutralizing antibodies have contributed to the rapid spread of this variant, posing a significant challenge to control the coronavirus disease 2019 (COVID-19) pandemic. There is, however, a silver lining for this wave of the Omicron variant. A lower risk of hospitalization and mortality has been observed in prevailing countries. Booster vaccination also has ameliorated a significant reduction in neutralization. Antiviral drugs are minimally influenced. Moreover, the functions of Fc-mediated and T-cell immunity have been retained to a great extent, both of which play a key role in preventing severe disease.
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Affiliation(s)
- Yifei Guo
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Shanghai Institute of Infectious Diseases and Biosecurity, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Jiajia Han
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Shanghai Institute of Infectious Diseases and Biosecurity, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Yao Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Shanghai Institute of Infectious Diseases and Biosecurity, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Jingjing He
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Shanghai Institute of Infectious Diseases and Biosecurity, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Weien Yu
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Shanghai Institute of Infectious Diseases and Biosecurity, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Xueyun Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Shanghai Institute of Infectious Diseases and Biosecurity, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Jingwen Wu
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Shanghai Institute of Infectious Diseases and Biosecurity, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Shenyan Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Shanghai Institute of Infectious Diseases and Biosecurity, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Yide Kong
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Shanghai Institute of Infectious Diseases and Biosecurity, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Yue Guo
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Shanghai Institute of Infectious Diseases and Biosecurity, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Yanxue Lin
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Shanghai Institute of Infectious Diseases and Biosecurity, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Jiming Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Shanghai Institute of Infectious Diseases and Biosecurity, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Medical Molecular Virology (MOE/MOH), Shanghai Medical College, Fudan University, Shanghai, China
- Department of Infectious Diseases, Jing’An Branch of Huashan Hospital, Fudan University, Shanghai, China
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571
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Sammartino JC, Cassaniti I, Ferrari A, Giardina F, Ferrari G, Zavaglio F, Paolucci S, Lilleri D, Piralla A, Baldanti F, Percivalle E. Evaluation of the Neutralizing Antibodies Response against 14 SARS-CoV-2 Variants in BNT162b2 Vaccinated Naïve and COVID-19 Positive Healthcare Workers from a Northern Italian Hospital. Vaccines (Basel) 2022; 10:vaccines10050703. [PMID: 35632457 PMCID: PMC9145000 DOI: 10.3390/vaccines10050703] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/22/2022] [Accepted: 04/27/2022] [Indexed: 11/24/2022] Open
Abstract
SARS-CoV-2 still represents a global health burden, causing more than six million deaths worldwide. Moreover, the emergence of new variants has posed new issues in terms of vaccine efficacy and immunogenicity. In this study, we aimed to evaluate the neutralizing antibody response against SARS-CoV-2 variants in different cohorts of vaccinated and unvaccinated subjects. Four-fold diluted sera from SARS-CoV-2 naïve and recovered subjects vaccinated with two or three doses of the BNT162b2 vaccine were challenged against 14 SARS-CoV-2 variants, and the SARS-CoV-2 neutralizing antibody titer was measured. Results were compared with those obtained from unvaccinated COVID-19 recovered patients. Overall, a better SARS-CoV-2 NT Abs response was observed in recovered vaccinated subjects after three doses of the vaccine when compared to unvaccinated patients and vaccinated subjects with only two doses. Additionally, the lowest level of response was observed against the Omicron variant. In conclusion, third doses of BNT162b2 vaccine seems to elicit a sustained response against the large majority of variants.
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Affiliation(s)
- Josè Camilla Sammartino
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy; (J.C.S.); (A.F.); (F.G.); (G.F.); (F.Z.); (S.P.); (D.L.); (A.P.); (F.B.); (E.P.)
| | - Irene Cassaniti
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy; (J.C.S.); (A.F.); (F.G.); (G.F.); (F.Z.); (S.P.); (D.L.); (A.P.); (F.B.); (E.P.)
- Correspondence:
| | - Alessandro Ferrari
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy; (J.C.S.); (A.F.); (F.G.); (G.F.); (F.Z.); (S.P.); (D.L.); (A.P.); (F.B.); (E.P.)
| | - Federica Giardina
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy; (J.C.S.); (A.F.); (F.G.); (G.F.); (F.Z.); (S.P.); (D.L.); (A.P.); (F.B.); (E.P.)
| | - Guglielmo Ferrari
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy; (J.C.S.); (A.F.); (F.G.); (G.F.); (F.Z.); (S.P.); (D.L.); (A.P.); (F.B.); (E.P.)
| | - Federica Zavaglio
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy; (J.C.S.); (A.F.); (F.G.); (G.F.); (F.Z.); (S.P.); (D.L.); (A.P.); (F.B.); (E.P.)
| | - Stefania Paolucci
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy; (J.C.S.); (A.F.); (F.G.); (G.F.); (F.Z.); (S.P.); (D.L.); (A.P.); (F.B.); (E.P.)
| | - Daniele Lilleri
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy; (J.C.S.); (A.F.); (F.G.); (G.F.); (F.Z.); (S.P.); (D.L.); (A.P.); (F.B.); (E.P.)
| | - Antonio Piralla
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy; (J.C.S.); (A.F.); (F.G.); (G.F.); (F.Z.); (S.P.); (D.L.); (A.P.); (F.B.); (E.P.)
| | - Fausto Baldanti
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy; (J.C.S.); (A.F.); (F.G.); (G.F.); (F.Z.); (S.P.); (D.L.); (A.P.); (F.B.); (E.P.)
- Department of Clinical, Surgical, Diagnostics and Pediatric Sciences, University of Pavia, 27100 Pavia, Italy
| | - Elena Percivalle
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy; (J.C.S.); (A.F.); (F.G.); (G.F.); (F.Z.); (S.P.); (D.L.); (A.P.); (F.B.); (E.P.)
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572
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SARS-CoV-2 Omicron variant: recent progress and future perspectives. Signal Transduct Target Ther 2022; 7:141. [PMID: 35484110 PMCID: PMC9047469 DOI: 10.1038/s41392-022-00997-x] [Citation(s) in RCA: 267] [Impact Index Per Article: 133.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/27/2022] [Accepted: 04/13/2022] [Indexed: 02/06/2023] Open
Abstract
Since the outbreak of the coronavirus disease 2019 (COVID-19) pandemic, there have been a few variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), one of which is the Omicron variant (B.1.1.529). The Omicron variant is the most mutated SARS-CoV-2 variant, and its high transmissibility and immune evasion ability have raised global concerns. Owing to its enhanced transmissibility, Omicron has rapidly replaced Delta as the dominant variant in several regions. However, recent studies have shown that the Omicron variant exhibits reduced pathogenicity due to altered cell tropism. In addition, Omicron exhibits significant resistance to the neutralizing activity of vaccines, convalescent serum, and most antibody therapies. In the present review, recent advances in the molecular and clinical characteristics of the infectivity, pathogenicity, and immune evasion of Omicron variant was summarized, and potential therapeutic applications in response to Omicron infection were discussed. Furthermore, we highlighted potential response to future waves and strategies to end the pandemic.
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573
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Ying B, Scheaffer SM, Whitener B, Liang CY, Dmytrenko O, Mackin S, Wu K, Lee D, Avena LE, Chong Z, Case JB, Ma L, Kim TTM, Sein CE, Woods A, Berrueta DM, Chang GY, Stewart-Jones G, Renzi I, Lai YT, Malinowski A, Carfi A, Elbashir SM, Edwards DK, Thackray LB, Diamond MS. Boosting with variant-matched or historical mRNA vaccines protects against Omicron infection in mice. Cell 2022; 185:1572-1587.e11. [PMID: 35452622 PMCID: PMC8958157 DOI: 10.1016/j.cell.2022.03.037] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/16/2022] [Accepted: 03/23/2022] [Indexed: 12/13/2022]
Abstract
The large number of spike substitutions in Omicron lineage variants (BA.1, BA.1.1., and BA.2) could jeopardize the efficacy of SARS-CoV-2 vaccines. We evaluated in mice the protective efficacy of the Moderna mRNA-1273 vaccine against BA.1 before or after boosting. Whereas two doses of mRNA-1273 vaccine induced high levels of neutralizing antibodies against historical WA1/2020 strains, lower levels against BA.1 were associated with breakthrough infection and inflammation in the lungs. A primary vaccination series with mRNA-1273.529, an Omicron-matched vaccine, potently neutralized BA.1 but inhibited historical or other SARS-CoV-2 variants less effectively. However, boosting with either mRNA-1273 or mRNA-1273.529 vaccines increased neutralizing titers and protection against BA.1 and BA.2 infection. Nonetheless, the neutralizing antibody titers were higher, and lung viral burden and cytokines were slightly lower in mice boosted with mRNA-1273.529 and challenged with BA.1. Thus, boosting with mRNA-1273 or mRNA-1273.529 enhances protection against Omicron infection with limited differences in efficacy measured.
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Affiliation(s)
- Baoling Ying
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Suzanne M Scheaffer
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Bradley Whitener
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Chieh-Yu Liang
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Oleksandr Dmytrenko
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Samantha Mackin
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Kai Wu
- Moderna, Inc., Cambridge, MA, USA
| | | | | | - Zhenlu Chong
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - James Brett Case
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Larissa B Thackray
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA; Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA; Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, Saint Louis, MO, USA.
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574
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Alkhatib M, Salpini R, Carioti L, Ambrosio FA, D’Anna S, Duca L, Costa G, Bellocchi MC, Piermatteo L, Artese A, Santoro MM, Alcaro S, Svicher V, Ceccherini-Silberstein F. Update on SARS-CoV-2 Omicron Variant of Concern and Its Peculiar Mutational Profile. Microbiol Spectr 2022; 10:e0273221. [PMID: 35352942 PMCID: PMC9045195 DOI: 10.1128/spectrum.02732-21] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 03/11/2022] [Indexed: 12/24/2022] Open
Abstract
The process of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genetic diversification is still ongoing and has very recently led to the emergence of a new variant of concern (VOC), defined as Omicron or B.1.1.529. Omicron VOC is the most divergent variant identified so far and has generated immediate concern for its potential capability to increase SARS-CoV-2 transmissibility and, more worryingly, to escape therapeutic and vaccine-induced antibodies. Nevertheless, a clear definition of the Omicron VOC mutational spectrum is still missing. Herein, we provide a comprehensive definition and functional characterization (in terms of infectivity and/or antigenicity) of mutations characterizing the Omicron VOC. In particular, 887,475 SARS-CoV-2 Omicron VOC whole-genome sequences were retrieved from the GISAID database and used to precisely define its specific patterns of mutations across the different viral proteins. In addition, the functional characterization of Omicron VOC spike mutations was finely discussed according to published manuscripts. Lastly, residues characterizing the Omicron VOC and the previous four VOCs (Alpha, Beta, Gamma, and Delta) were mapped on the three-dimensional structure of the SARS-CoV-2 spike protein to assess their localization in the different spike domains. Overall, our study will assist with deciphering the Omicron VOC mutational profile and will shed more light on its clinical implications. This is critical considering that Omicron VOC is currently the predominant variant worldwide. IMPORTANCE The Omicron variant of concern (VOC) has a peculiar spectrum of mutations characterized by the acquisition of mutations or deletions rarely detected in previously identified variants, particularly in the spike glycoprotein. Such mutations, mostly residing in the receptor-binding domain, could play a pivotal role in enhancing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infectivity (by increasing binding affinity for ACE2), jeopardizing spike recognition by therapeutic and vaccine-induced antibodies and causing diagnostic assay failure. To our knowledge, this is one of the first exhaustive descriptions of newly emerged mutations underlying the Omicron VOC and its biological and clinical implications.
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Affiliation(s)
- Mohammad Alkhatib
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Romina Salpini
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Luca Carioti
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Francesca Alessandra Ambrosio
- Dipartimento di Scienze della Salute, Università degli Studi “Magna Graecia” di Catanzaro, Campus S. Venuta, Catanzaro, Italy
| | - Stefano D’Anna
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Leonardo Duca
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Giosuè Costa
- Dipartimento di Scienze della Salute, Università degli Studi “Magna Graecia” di Catanzaro, Campus S. Venuta, Catanzaro, Italy
- Net4Science Academic Spin-Off, Università Magna Græcia di Catanzaro, Campus S. Venuta, Catanzaro, Italy
| | | | - Lorenzo Piermatteo
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Anna Artese
- Dipartimento di Scienze della Salute, Università degli Studi “Magna Graecia” di Catanzaro, Campus S. Venuta, Catanzaro, Italy
- Net4Science Academic Spin-Off, Università Magna Græcia di Catanzaro, Campus S. Venuta, Catanzaro, Italy
| | | | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Università degli Studi “Magna Graecia” di Catanzaro, Campus S. Venuta, Catanzaro, Italy
- Net4Science Academic Spin-Off, Università Magna Græcia di Catanzaro, Campus S. Venuta, Catanzaro, Italy
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575
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Du W, Hurdiss DL, Drabek D, Mykytyn AZ, Kaiser FK, González-Hernández M, Muñoz-Santos D, Lamers MM, van Haperen R, Li W, Drulyte I, Wang C, Sola I, Armando F, Beythien G, Ciurkiewicz M, Baumgärtner W, Guilfoyle K, Smits T, van der Lee J, van Kuppeveld FJM, van Amerongen G, Haagmans BL, Enjuanes L, Osterhaus ADME, Grosveld F, Bosch BJ. An ACE2-blocking antibody confers broad neutralization and protection against Omicron and other SARS-CoV-2 variants of concern. Sci Immunol 2022; 7:eabp9312. [PMID: 35471062 PMCID: PMC9097884 DOI: 10.1126/sciimmunol.abp9312] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The ongoing evolution of SARS-CoV-2 has resulted in the emergence of Omicron, which displays striking immune escape potential through mutations at key antigenic sites on the spike protein. Many of these mutations localize to the spike protein ACE2 receptor-binding domain, annulling the neutralizing activity of therapeutic antibodies that were effective against other Variants of Concern (VOCs) earlier in the pandemic. Here, we identified a receptor-blocking human monoclonal antibody, 87G7, that retained potent in vitro neutralizing activity against SARS-CoV-2 variants including the Alpha, Beta, Gamma, Delta and Omicron (BA.1/BA.2) VOCs. Using cryo-electron microscopy and site-directed mutagenesis experiments, we showed that 87G7 targets a patch of hydrophobic residues in the ACE2-binding site that are highly conserved in SARS-CoV-2 variants, explaining its broad neutralization capacity. 87G7 protected mice and/or hamsters prophylactically against challenge with all current SARS-CoV-2 VOCs, and showed therapeutic activity against SARS-CoV-2 challenge in both animal models. Our findings demonstrate that 87G7 holds promise as a prophylactic or therapeutic agent for COVID-19 that is more resilient to SARS-CoV-2 antigenic diversity.
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Affiliation(s)
- Wenjuan Du
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Daniel L Hurdiss
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Dubravka Drabek
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, the Netherlands.,Harbour BioMed, Rotterdam, the Netherlands
| | - Anna Z Mykytyn
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Franziska K Kaiser
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Mariana González-Hernández
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Diego Muñoz-Santos
- Department of Molecular and Cell Biology, National Center for Biotechnology-Spanish National Research Council (CNB-CSIC), Madrid, Spain
| | - Mart M Lamers
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Rien van Haperen
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, the Netherlands.,Harbour BioMed, Rotterdam, the Netherlands
| | - Wentao Li
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Ieva Drulyte
- Thermo Fisher Scientific, Materials and Structural Analysis, Eindhoven, the Netherlands
| | - Chunyan Wang
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Isabel Sola
- Department of Molecular and Cell Biology, National Center for Biotechnology-Spanish National Research Council (CNB-CSIC), Madrid, Spain
| | - Federico Armando
- Department of Pathology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Georg Beythien
- Department of Pathology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Malgorzata Ciurkiewicz
- Department of Pathology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Wolfgang Baumgärtner
- Department of Pathology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | | | - Tony Smits
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Joline van der Lee
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Frank J M van Kuppeveld
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | | | - Bart L Haagmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Luis Enjuanes
- Department of Molecular and Cell Biology, National Center for Biotechnology-Spanish National Research Council (CNB-CSIC), Madrid, Spain
| | - Albert D M E Osterhaus
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany.,Global Virus Network, Center of Excellence
| | - Frank Grosveld
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, the Netherlands.,Harbour BioMed, Rotterdam, the Netherlands
| | - Berend-Jan Bosch
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
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576
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Ballesteros-Sanabria L, Pelaez-Prestel HF, Ras-Carmona A, Reche PA. Resilience of Spike-Specific Immunity Induced by COVID-19 Vaccines against SARS-CoV-2 Variants. Biomedicines 2022; 10:biomedicines10050996. [PMID: 35625733 PMCID: PMC9138591 DOI: 10.3390/biomedicines10050996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 04/20/2022] [Accepted: 04/22/2022] [Indexed: 12/10/2022] Open
Abstract
The outbreak of SARS-CoV-2 leading to the declaration of the COVID-19 global pandemic has led to the urgent development and deployment of several COVID-19 vaccines. Many of these new vaccines, including those based on mRNA and adenoviruses, are aimed to generate neutralizing antibodies against the spike glycoprotein, which is known to bind to the receptor angiotensin converting enzyme 2 (ACE2) in host cells via the receptor-binding domain (RBD). Antibodies binding to this domain can block the interaction with the receptor and prevent viral entry into the cells. Additionally, these vaccines can also induce spike-specific T cells which could contribute to providing protection against the virus. However, the emergence of new SARS-CoV-2 variants can impair the immunity generated by COVID-19 vaccines if mutations occur in cognate epitopes, precluding immune recognition. Here, we evaluated the chance of five SARS-CoV-2 variants of concern (VOCs), Alpha, Beta, Gamma, Delta and Omicron, to escape spike-specific immunity induced by vaccines. To that end, we examined the impact of the SARS-CoV-2 variant mutations on residues located on experimentally verified spike-specific epitopes, deposited at the Immune Epitope Database, that are targeted by neutralizing antibodies or recognized by T cells. We found about 300 of such B cell epitopes, which were largely overlapping, and could be grouped into 54 B cell epitope clusters sharing ≥ 7 residues. Most of the B cell epitope clusters map in the RBD domain (39 out of 54) and 20%, 50%, 37%, 44% and 57% of the total are mutated in SARS-CoV-2 Alpha, Beta, Gamma, Delta and Omicron variants, respectively. We also found 234 experimentally verified CD8 and CD4 T cell epitopes that were distributed evenly throughout the spike protein. Interestingly, in each SARS-CoV-2 VOC, over 87% and 79% of CD8 and CD4 T cell epitopes, respectively, are not mutated. These observations suggest that SARS-CoV-2 VOCs—particularly the Omicron variant—may be prone to escape spike-specific antibody immunity, but not cellular immunity, elicited by COVID-19 vaccines.
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577
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Ikemura N, Taminishi S, Inaba T, Arimori T, Motooka D, Katoh K, Kirita Y, Higuchi Y, Li S, Suzuki T, Itoh Y, Ozaki Y, Nakamura S, Matoba S, Standley DM, Okamoto T, Takagi J, Hoshino A. An engineered ACE2 decoy neutralizes the SARS-CoV-2 Omicron variant and confers protection against infection in vivo. Sci Transl Med 2022; 14:eabn7737. [PMID: 35471044 PMCID: PMC9097879 DOI: 10.1126/scitranslmed.abn7737] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The Omicron (B.1.1.529) SARS-CoV-2 variant contains an unusually high number of mutations in the spike protein, raising concerns of escape from vaccines, convalescent serum and therapeutic drugs. Here we analyzed the degree to which Omicron pseudovirus evades neutralization by serum or therapeutic antibodies. Serum samples obtained 3 months after two doses of BNT162b2 vaccination exhibited 18-fold lower neutralization titers against Omicron than parental virus. Convalescent serum samples from individuals infected with the Alpha and Delta variants allowed similar frequencies of Omicron breakthrough infections. Domain-wise analysis using chimeric spike proteins revealed that this efficient evasion was primarily achieved by mutations clustered in the receptor-binding domain, but that multiple mutations in the N-terminal domain contributed as well. Omicron escaped a therapeutic cocktail of imdevimab and casirivimab, whereas sotrovimab, which targets a conserved region to avoid viral mutation, remains effective. Angiotensin-converting enzyme 2 (ACE2) decoys are another virus-neutralizing drug modality that are free, at least in theory, from complete escape. Deep mutational analysis demonstrated that, indeed, an engineered ACE2 molecule prevented escape for each single-residue mutation in the receptor-binding domain, similar to immunized serum. Engineered ACE2 neutralized Omicron comparably to the Wuhan strain and also showed a therapeutic effect against Omicron infection in hamsters and human ACE2 transgenic mice. Like previous SARS-CoV-2 variants, some sarbecoviruses showed high sensitivity against engineered ACE2, confirming the therapeutic value against diverse variants, including those that are yet to emerge.
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Affiliation(s)
- Nariko Ikemura
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Shunta Taminishi
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Tohru Inaba
- Department of Infection Control and Molecular Laboratory Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Takao Arimori
- Laboratory for Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Daisuke Motooka
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan.,Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Osaka 565-0871, Japan
| | - Kazutaka Katoh
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan.,Department of Systems Immunology, Immunology Frontier Research Center (IFReC), Osaka University, Osaka 565-0871, Japan
| | - Yuhei Kirita
- Department of Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Yusuke Higuchi
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Songling Li
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan.,Department of Systems Immunology, Immunology Frontier Research Center (IFReC), Osaka University, Osaka 565-0871, Japan
| | - Tatsuya Suzuki
- Institute for Advanced Co-Creation Studies, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Yumi Itoh
- Institute for Advanced Co-Creation Studies, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Yuki Ozaki
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Shota Nakamura
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan.,Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Osaka 565-0871, Japan.,Center for Infectious Disease Education and Research (CiDER), Osaka University, Osaka 565-0871, Japan
| | - Satoaki Matoba
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Daron M Standley
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan.,Department of Systems Immunology, Immunology Frontier Research Center (IFReC), Osaka University, Osaka 565-0871, Japan.,Center for Infectious Disease Education and Research (CiDER), Osaka University, Osaka 565-0871, Japan
| | - Toru Okamoto
- Institute for Advanced Co-Creation Studies, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan.,Center for Infectious Disease Education and Research (CiDER), Osaka University, Osaka 565-0871, Japan
| | - Junichi Takagi
- Laboratory for Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan.,Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Osaka 565-0871, Japan.,Center for Infectious Disease Education and Research (CiDER), Osaka University, Osaka 565-0871, Japan
| | - Atsushi Hoshino
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
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578
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Zhou B, Song S, Guo H, Zhou X, Fan Q, Liu W, Cheng L, Ge X, Ju B, Zhang Z. A fourth dose of Omicron RBD vaccine enhances broad neutralization against SARS-CoV-2 variants including BA.1 and BA.2 in vaccinated mice. J Med Virol 2022; 94:3992-3997. [PMID: 35474319 PMCID: PMC9088529 DOI: 10.1002/jmv.27811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 04/23/2022] [Accepted: 04/25/2022] [Indexed: 11/25/2022]
Abstract
The SARS‐CoV‐2 vaccines have been widely used to build an immunologic barrier in the population against the COVID‐19 pandemic. However, a newly emerging Omicron variant, including BA.1, BA.1.1, BA.2, and BA.3 sublineages, largely escaped the neutralization of existing neutralizing antibodies (nAbs), even those elicited by three doses of vaccines. Here, we used the Omicron BA.1 RBD as a fourth dose of vaccine to induce potent Omicron‐specific nAbs and evaluated the broadly neutralizing activities against SARS‐CoV‐2 variants. The BA.1‐based vaccine was indeed prone to induce a strain‐specific antibody response substantially cross‐reactive with BA.2 sublineage, and yet triggered broad neutralization against SARS‐CoV‐2 variants when it was used in the sequential immunization with WT and other variant vaccines. These results demonstrated that the booster of Omicron RBD vaccine could be a rational strategy to enhance the broadly nAb response.
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Affiliation(s)
- Bing Zhou
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital; The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, 518112, Guangdong Province, China
| | - Shuo Song
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital; The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, 518112, Guangdong Province, China
| | - Huimin Guo
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital; The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, 518112, Guangdong Province, China
| | - Xinrong Zhou
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital; The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, 518112, Guangdong Province, China
| | - Qing Fan
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital; The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, 518112, Guangdong Province, China
| | - Weilong Liu
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital; The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, 518112, Guangdong Province, China
| | - Lin Cheng
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital; The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, 518112, Guangdong Province, China
| | - Xiangyang Ge
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital; The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, 518112, Guangdong Province, China
| | - Bin Ju
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital; The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, 518112, Guangdong Province, China.,Guangdong Key laboratory for anti-infection Drug Quality Evaluation, Shenzhen, 518112, Guangdong Province, China
| | - Zheng Zhang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital; The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, 518112, Guangdong Province, China.,Guangdong Key laboratory for anti-infection Drug Quality Evaluation, Shenzhen, 518112, Guangdong Province, China.,Shenzhen Research Center for Communicable Disease Diagnosis and Treatment of Chinese Academy of Medical Science, Shenzhen, 518112, Guangdong Province, China
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579
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Yuan S, Jiang SC, Zhang ZW, Fu YF, Yang XY, Li ZL, Hu J, Du JB, Yuan M, Chen YE. Surface electrostatic shift on spike protein decreased antibody activities against SARS-CoV-2 Omicron variant. J Infect 2022; 85:174-211. [PMID: 35472368 PMCID: PMC9035662 DOI: 10.1016/j.jinf.2022.04.033] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 04/16/2022] [Accepted: 04/19/2022] [Indexed: 11/19/2022]
Affiliation(s)
- Shu Yuan
- College of Resources, Sichuan Agricultural University, Chengdu, China.
| | - Si-Cong Jiang
- Haisco Pharmaceutical Group Comp. Ltd., Chengdu, China
| | - Zhong-Wei Zhang
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Yu-Fan Fu
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Xin-Yue Yang
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Zi-Lin Li
- Department of Cardiovascular Surgery, Xijing Hospital, Medical University of the Air Force, Xi'an, China
| | - Jing Hu
- School of Medicine, Northwest University, Xi'an 710069, China
| | - Jun-Bo Du
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Ming Yuan
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Yang-Er Chen
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China
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580
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Favresse J, Dogné JM, Douxfils J. Assessment of the humoral response in Omicron breakthrough cases in healthcare workers who received the BNT162b2 booster. Clin Chem Lab Med 2022; 60:e153-e156. [PMID: 35452575 DOI: 10.1515/cclm-2022-0323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 04/09/2022] [Indexed: 12/20/2022]
Affiliation(s)
- Julien Favresse
- Department of Laboratory Medicine, Clinique Saint-Luc Bouge, Namur, Bouge, Belgium.,Department of Pharmacy, University of Namur, Namur Research Institute for Life Sciences, Namur, Belgium
| | - Jean-Michel Dogné
- Department of Pharmacy, University of Namur, Namur Research Institute for Life Sciences, Namur, Belgium
| | - Jonathan Douxfils
- Department of Pharmacy, University of Namur, Namur Research Institute for Life Sciences, Namur, Belgium.,Qualiblood s.a., Namur, Belgium
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581
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Zhou T, Wang L, Misasi J, Pegu A, Zhang Y, Harris DR, Olia AS, Talana CA, Yang ES, Chen M, Choe M, Shi W, Teng IT, Creanga A, Jenkins C, Leung K, Liu T, Stancofski ESD, Stephens T, Zhang B, Tsybovsky Y, Graham BS, Mascola JR, Sullivan NJ, Kwong PD. Structural basis for potent antibody neutralization of SARS-CoV-2 variants including B.1.1.529. Science 2022; 376:eabn8897. [PMID: 35324257 PMCID: PMC9580340 DOI: 10.1126/science.abn8897] [Citation(s) in RCA: 104] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 03/19/2022] [Indexed: 12/14/2022]
Abstract
The rapid spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) B.1.1.529 (Omicron) variant and its resistance to neutralization by vaccinee and convalescent sera are driving a search for monoclonal antibodies with potent neutralization. To provide insight into effective neutralization, we determined cryo-electron microscopy structures and evaluated receptor binding domain (RBD) antibodies for their ability to bind and neutralize B.1.1.529. Mutations altered 16% of the B.1.1.529 RBD surface, clustered on an RBD ridge overlapping the angiotensin-converting enzyme 2 (ACE2)-binding surface and reduced binding of most antibodies. Substantial inhibitory activity was retained by select monoclonal antibodies-including A23-58.1, B1-182.1, COV2-2196, S2E12, A19-46.1, S309, and LY-CoV1404-that accommodated these changes and neutralized B.1.1.529. We identified combinations of antibodies with synergistic neutralization. The analysis revealed structural mechanisms for maintenance of potent neutralization against emerging variants.
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Affiliation(s)
- Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lingshu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - John Misasi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amarendra Pegu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yi Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Darcy R. Harris
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adam S. Olia
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chloe Adrienna Talana
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eun Sung Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Man Chen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Misook Choe
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wei Shi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - I-Ting Teng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adrian Creanga
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Claudia Jenkins
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Kwanyee Leung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tracy Liu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Erik-Stephane D. Stancofski
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tyler Stephens
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yaroslav Tsybovsky
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Barney S. Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - John R. Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nancy J. Sullivan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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582
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Waxman JG, Makov-Assif M, Reis BY, Netzer D, Balicer RD, Dagan N, Barda N. Comparing COVID-19-related hospitalization rates among individuals with infection-induced and vaccine-induced immunity in Israel. Nat Commun 2022; 13:2202. [PMID: 35459237 PMCID: PMC9033865 DOI: 10.1038/s41467-022-29858-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 03/30/2022] [Indexed: 11/09/2022] Open
Abstract
With the COVID-19 pandemic ongoing, accurate assessment of population immunity and the effectiveness of booster and enhancer vaccine doses is critical. We compare COVID-19-related hospitalization incidence rates in 2,412,755 individuals across four exposure levels: non-recent vaccine immunity (two BNT162b2 COVID-19 vaccine doses five or more months prior), boosted vaccine immunity (three BNT162b2 doses), infection-induced immunity (previous COVID-19 without a subsequent BNT162b2 dose), and enhanced infection-induced immunity (previous COVID-19 with a subsequent BNT162b2 dose). Rates, adjusted for potential demographic, clinical and health-seeking-behavior confounders, were assessed from July-November 2021 when the Delta variant was predominant. Compared with non-recent vaccine immunity, COVID-19-related hospitalization incidence rates were reduced by 89% (87–91%) for boosted vaccine immunity, 66% (50–77%) for infection-induced immunity and 75% (61–83%) for enhanced infection-induced immunity. We demonstrate that infection-induced immunity (enhanced or not) provides more protection against COVID-19-related hospitalization than non-recent vaccine immunity, but less protection than booster vaccination. Additionally, our results suggest that vaccinating individuals with infection-induced immunity further enhances their protection. The relative degree of immunity to SARS-CoV-2 provided by combinations of natural infection, vaccination, and booster doses is unknown. Here, the authors show that infection-induced immunity provides more protection against COVID-19-related hospitalization than non-recent vaccine immunity, but less than booster vaccination.
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Affiliation(s)
- Jacob G Waxman
- Clalit Research Institute, Innovation Division, Clalit Health Services, Tel Aviv, Israel.
| | - Maya Makov-Assif
- Clalit Research Institute, Innovation Division, Clalit Health Services, Tel Aviv, Israel
| | - Ben Y Reis
- Predictive Medicine Group, Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA.,The Ivan and Francesca Berkowitz Family Living Laboratory Collaboration at Harvard Medical School and Clalit Research Institute, Boston, MA, USA
| | - Doron Netzer
- Community Medical Services Division, Clalit Health Services, Tel Aviv, Israel
| | - Ran D Balicer
- Clalit Research Institute, Innovation Division, Clalit Health Services, Tel Aviv, Israel.,The Ivan and Francesca Berkowitz Family Living Laboratory Collaboration at Harvard Medical School and Clalit Research Institute, Boston, MA, USA.,School of Public Health, Faculty of Health Sciences, Ben Gurion University of the Negev, Be'er Sheva, Israel
| | - Noa Dagan
- Clalit Research Institute, Innovation Division, Clalit Health Services, Tel Aviv, Israel.,The Ivan and Francesca Berkowitz Family Living Laboratory Collaboration at Harvard Medical School and Clalit Research Institute, Boston, MA, USA.,Software and Information Systems Engineering, Ben Gurion University, Be'er Sheva, Israel.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Noam Barda
- Software and Information Systems Engineering, Ben Gurion University, Be'er Sheva, Israel.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.,Arc Innovation Center, Sheba Medical Center, Ramat-Gan, Israel
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583
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Andrews N, Stowe J, Kirsebom F, Toffa S, Rickeard T, Gallagher E, Gower C, Kall M, Groves N, O'Connell AM, Simons D, Blomquist PB, Zaidi A, Nash S, Iwani Binti Abdul Aziz N, Thelwall S, Dabrera G, Myers R, Amirthalingam G, Gharbia S, Barrett JC, Elson R, Ladhani SN, Ferguson N, Zambon M, Campbell CNJ, Brown K, Hopkins S, Chand M, Ramsay M, Lopez Bernal J. Covid-19 Vaccine Effectiveness against the Omicron (B.1.1.529) Variant. N Engl J Med 2022; 386:1532-1546. [PMID: 35249272 DOI: 10.1101/2021.12.14.21267615] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
BACKGROUND A rapid increase in coronavirus disease 2019 (Covid-19) cases due to the omicron (B.1.1.529) variant of severe acute respiratory syndrome coronavirus 2 in highly vaccinated populations has aroused concerns about the effectiveness of current vaccines. METHODS We used a test-negative case-control design to estimate vaccine effectiveness against symptomatic disease caused by the omicron and delta (B.1.617.2) variants in England. Vaccine effectiveness was calculated after primary immunization with two doses of BNT162b2 (Pfizer-BioNTech), ChAdOx1 nCoV-19 (AstraZeneca), or mRNA-1273 (Moderna) vaccine and after a booster dose of BNT162b2, ChAdOx1 nCoV-19, or mRNA-1273. RESULTS Between November 27, 2021, and January 12, 2022, a total of 886,774 eligible persons infected with the omicron variant, 204,154 eligible persons infected with the delta variant, and 1,572,621 eligible test-negative controls were identified. At all time points investigated and for all combinations of primary course and booster vaccines, vaccine effectiveness against symptomatic disease was higher for the delta variant than for the omicron variant. No effect against the omicron variant was noted from 20 weeks after two ChAdOx1 nCoV-19 doses, whereas vaccine effectiveness after two BNT162b2 doses was 65.5% (95% confidence interval [CI], 63.9 to 67.0) at 2 to 4 weeks, dropping to 8.8% (95% CI, 7.0 to 10.5) at 25 or more weeks. Among ChAdOx1 nCoV-19 primary course recipients, vaccine effectiveness increased to 62.4% (95% CI, 61.8 to 63.0) at 2 to 4 weeks after a BNT162b2 booster before decreasing to 39.6% (95% CI, 38.0 to 41.1) at 10 or more weeks. Among BNT162b2 primary course recipients, vaccine effectiveness increased to 67.2% (95% CI, 66.5 to 67.8) at 2 to 4 weeks after a BNT162b2 booster before declining to 45.7% (95% CI, 44.7 to 46.7) at 10 or more weeks. Vaccine effectiveness after a ChAdOx1 nCoV-19 primary course increased to 70.1% (95% CI, 69.5 to 70.7) at 2 to 4 weeks after an mRNA-1273 booster and decreased to 60.9% (95% CI, 59.7 to 62.1) at 5 to 9 weeks. After a BNT162b2 primary course, the mRNA-1273 booster increased vaccine effectiveness to 73.9% (95% CI, 73.1 to 74.6) at 2 to 4 weeks; vaccine effectiveness fell to 64.4% (95% CI, 62.6 to 66.1) at 5 to 9 weeks. CONCLUSIONS Primary immunization with two doses of ChAdOx1 nCoV-19 or BNT162b2 vaccine provided limited protection against symptomatic disease caused by the omicron variant. A BNT162b2 or mRNA-1273 booster after either the ChAdOx1 nCoV-19 or BNT162b2 primary course substantially increased protection, but that protection waned over time. (Funded by the U.K. Health Security Agency.).
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Affiliation(s)
- Nick Andrews
- From the U.K. Health Security Agency (N.A., J.S., F.K., S. Toffa, T.R., E.G., C.G., M.K., N.G., A.-M.O., D.S., P.B.B., A.Z., S.N., N.I.B.A.A., S. Thelwall, G.D., R.M., G.A., S.G., R.E., S.N.L., M.Z., C.N.J.C., K.B., S.H., M.C., M.R., J.L.B.), the National Institute for Health Research (NIHR) Health Protection Research Unit in Vaccines and Immunisation, London School of Hygiene and Tropical Medicine (N.A., G.A., C.N.J.C., K.B., M.R., J.L.B.), the Paediatric Infectious Diseases Research Group, St. George's University of London (R.M., S.N.L.), the Medical Research Council Centre for Global Infectious Disease Analysis (N.F.) and the NIHR Health Protection Research Unit in Respiratory Infections (N.F., M.Z., J.L.B.), Imperial College London, and Guy's and St. Thomas's Hospital NHS Trust (M.C.), London, Wellcome Sanger Institute, Hinxton (J.C.B.), and Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford (S.H.) - all in the United Kingdom
| | - Julia Stowe
- From the U.K. Health Security Agency (N.A., J.S., F.K., S. Toffa, T.R., E.G., C.G., M.K., N.G., A.-M.O., D.S., P.B.B., A.Z., S.N., N.I.B.A.A., S. Thelwall, G.D., R.M., G.A., S.G., R.E., S.N.L., M.Z., C.N.J.C., K.B., S.H., M.C., M.R., J.L.B.), the National Institute for Health Research (NIHR) Health Protection Research Unit in Vaccines and Immunisation, London School of Hygiene and Tropical Medicine (N.A., G.A., C.N.J.C., K.B., M.R., J.L.B.), the Paediatric Infectious Diseases Research Group, St. George's University of London (R.M., S.N.L.), the Medical Research Council Centre for Global Infectious Disease Analysis (N.F.) and the NIHR Health Protection Research Unit in Respiratory Infections (N.F., M.Z., J.L.B.), Imperial College London, and Guy's and St. Thomas's Hospital NHS Trust (M.C.), London, Wellcome Sanger Institute, Hinxton (J.C.B.), and Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford (S.H.) - all in the United Kingdom
| | - Freja Kirsebom
- From the U.K. Health Security Agency (N.A., J.S., F.K., S. Toffa, T.R., E.G., C.G., M.K., N.G., A.-M.O., D.S., P.B.B., A.Z., S.N., N.I.B.A.A., S. Thelwall, G.D., R.M., G.A., S.G., R.E., S.N.L., M.Z., C.N.J.C., K.B., S.H., M.C., M.R., J.L.B.), the National Institute for Health Research (NIHR) Health Protection Research Unit in Vaccines and Immunisation, London School of Hygiene and Tropical Medicine (N.A., G.A., C.N.J.C., K.B., M.R., J.L.B.), the Paediatric Infectious Diseases Research Group, St. George's University of London (R.M., S.N.L.), the Medical Research Council Centre for Global Infectious Disease Analysis (N.F.) and the NIHR Health Protection Research Unit in Respiratory Infections (N.F., M.Z., J.L.B.), Imperial College London, and Guy's and St. Thomas's Hospital NHS Trust (M.C.), London, Wellcome Sanger Institute, Hinxton (J.C.B.), and Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford (S.H.) - all in the United Kingdom
| | - Samuel Toffa
- From the U.K. Health Security Agency (N.A., J.S., F.K., S. Toffa, T.R., E.G., C.G., M.K., N.G., A.-M.O., D.S., P.B.B., A.Z., S.N., N.I.B.A.A., S. Thelwall, G.D., R.M., G.A., S.G., R.E., S.N.L., M.Z., C.N.J.C., K.B., S.H., M.C., M.R., J.L.B.), the National Institute for Health Research (NIHR) Health Protection Research Unit in Vaccines and Immunisation, London School of Hygiene and Tropical Medicine (N.A., G.A., C.N.J.C., K.B., M.R., J.L.B.), the Paediatric Infectious Diseases Research Group, St. George's University of London (R.M., S.N.L.), the Medical Research Council Centre for Global Infectious Disease Analysis (N.F.) and the NIHR Health Protection Research Unit in Respiratory Infections (N.F., M.Z., J.L.B.), Imperial College London, and Guy's and St. Thomas's Hospital NHS Trust (M.C.), London, Wellcome Sanger Institute, Hinxton (J.C.B.), and Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford (S.H.) - all in the United Kingdom
| | - Tim Rickeard
- From the U.K. Health Security Agency (N.A., J.S., F.K., S. Toffa, T.R., E.G., C.G., M.K., N.G., A.-M.O., D.S., P.B.B., A.Z., S.N., N.I.B.A.A., S. Thelwall, G.D., R.M., G.A., S.G., R.E., S.N.L., M.Z., C.N.J.C., K.B., S.H., M.C., M.R., J.L.B.), the National Institute for Health Research (NIHR) Health Protection Research Unit in Vaccines and Immunisation, London School of Hygiene and Tropical Medicine (N.A., G.A., C.N.J.C., K.B., M.R., J.L.B.), the Paediatric Infectious Diseases Research Group, St. George's University of London (R.M., S.N.L.), the Medical Research Council Centre for Global Infectious Disease Analysis (N.F.) and the NIHR Health Protection Research Unit in Respiratory Infections (N.F., M.Z., J.L.B.), Imperial College London, and Guy's and St. Thomas's Hospital NHS Trust (M.C.), London, Wellcome Sanger Institute, Hinxton (J.C.B.), and Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford (S.H.) - all in the United Kingdom
| | - Eileen Gallagher
- From the U.K. Health Security Agency (N.A., J.S., F.K., S. Toffa, T.R., E.G., C.G., M.K., N.G., A.-M.O., D.S., P.B.B., A.Z., S.N., N.I.B.A.A., S. Thelwall, G.D., R.M., G.A., S.G., R.E., S.N.L., M.Z., C.N.J.C., K.B., S.H., M.C., M.R., J.L.B.), the National Institute for Health Research (NIHR) Health Protection Research Unit in Vaccines and Immunisation, London School of Hygiene and Tropical Medicine (N.A., G.A., C.N.J.C., K.B., M.R., J.L.B.), the Paediatric Infectious Diseases Research Group, St. George's University of London (R.M., S.N.L.), the Medical Research Council Centre for Global Infectious Disease Analysis (N.F.) and the NIHR Health Protection Research Unit in Respiratory Infections (N.F., M.Z., J.L.B.), Imperial College London, and Guy's and St. Thomas's Hospital NHS Trust (M.C.), London, Wellcome Sanger Institute, Hinxton (J.C.B.), and Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford (S.H.) - all in the United Kingdom
| | - Charlotte Gower
- From the U.K. Health Security Agency (N.A., J.S., F.K., S. Toffa, T.R., E.G., C.G., M.K., N.G., A.-M.O., D.S., P.B.B., A.Z., S.N., N.I.B.A.A., S. Thelwall, G.D., R.M., G.A., S.G., R.E., S.N.L., M.Z., C.N.J.C., K.B., S.H., M.C., M.R., J.L.B.), the National Institute for Health Research (NIHR) Health Protection Research Unit in Vaccines and Immunisation, London School of Hygiene and Tropical Medicine (N.A., G.A., C.N.J.C., K.B., M.R., J.L.B.), the Paediatric Infectious Diseases Research Group, St. George's University of London (R.M., S.N.L.), the Medical Research Council Centre for Global Infectious Disease Analysis (N.F.) and the NIHR Health Protection Research Unit in Respiratory Infections (N.F., M.Z., J.L.B.), Imperial College London, and Guy's and St. Thomas's Hospital NHS Trust (M.C.), London, Wellcome Sanger Institute, Hinxton (J.C.B.), and Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford (S.H.) - all in the United Kingdom
| | - Meaghan Kall
- From the U.K. Health Security Agency (N.A., J.S., F.K., S. Toffa, T.R., E.G., C.G., M.K., N.G., A.-M.O., D.S., P.B.B., A.Z., S.N., N.I.B.A.A., S. Thelwall, G.D., R.M., G.A., S.G., R.E., S.N.L., M.Z., C.N.J.C., K.B., S.H., M.C., M.R., J.L.B.), the National Institute for Health Research (NIHR) Health Protection Research Unit in Vaccines and Immunisation, London School of Hygiene and Tropical Medicine (N.A., G.A., C.N.J.C., K.B., M.R., J.L.B.), the Paediatric Infectious Diseases Research Group, St. George's University of London (R.M., S.N.L.), the Medical Research Council Centre for Global Infectious Disease Analysis (N.F.) and the NIHR Health Protection Research Unit in Respiratory Infections (N.F., M.Z., J.L.B.), Imperial College London, and Guy's and St. Thomas's Hospital NHS Trust (M.C.), London, Wellcome Sanger Institute, Hinxton (J.C.B.), and Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford (S.H.) - all in the United Kingdom
| | - Natalie Groves
- From the U.K. Health Security Agency (N.A., J.S., F.K., S. Toffa, T.R., E.G., C.G., M.K., N.G., A.-M.O., D.S., P.B.B., A.Z., S.N., N.I.B.A.A., S. Thelwall, G.D., R.M., G.A., S.G., R.E., S.N.L., M.Z., C.N.J.C., K.B., S.H., M.C., M.R., J.L.B.), the National Institute for Health Research (NIHR) Health Protection Research Unit in Vaccines and Immunisation, London School of Hygiene and Tropical Medicine (N.A., G.A., C.N.J.C., K.B., M.R., J.L.B.), the Paediatric Infectious Diseases Research Group, St. George's University of London (R.M., S.N.L.), the Medical Research Council Centre for Global Infectious Disease Analysis (N.F.) and the NIHR Health Protection Research Unit in Respiratory Infections (N.F., M.Z., J.L.B.), Imperial College London, and Guy's and St. Thomas's Hospital NHS Trust (M.C.), London, Wellcome Sanger Institute, Hinxton (J.C.B.), and Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford (S.H.) - all in the United Kingdom
| | - Anne-Marie O'Connell
- From the U.K. Health Security Agency (N.A., J.S., F.K., S. Toffa, T.R., E.G., C.G., M.K., N.G., A.-M.O., D.S., P.B.B., A.Z., S.N., N.I.B.A.A., S. Thelwall, G.D., R.M., G.A., S.G., R.E., S.N.L., M.Z., C.N.J.C., K.B., S.H., M.C., M.R., J.L.B.), the National Institute for Health Research (NIHR) Health Protection Research Unit in Vaccines and Immunisation, London School of Hygiene and Tropical Medicine (N.A., G.A., C.N.J.C., K.B., M.R., J.L.B.), the Paediatric Infectious Diseases Research Group, St. George's University of London (R.M., S.N.L.), the Medical Research Council Centre for Global Infectious Disease Analysis (N.F.) and the NIHR Health Protection Research Unit in Respiratory Infections (N.F., M.Z., J.L.B.), Imperial College London, and Guy's and St. Thomas's Hospital NHS Trust (M.C.), London, Wellcome Sanger Institute, Hinxton (J.C.B.), and Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford (S.H.) - all in the United Kingdom
| | - David Simons
- From the U.K. Health Security Agency (N.A., J.S., F.K., S. Toffa, T.R., E.G., C.G., M.K., N.G., A.-M.O., D.S., P.B.B., A.Z., S.N., N.I.B.A.A., S. Thelwall, G.D., R.M., G.A., S.G., R.E., S.N.L., M.Z., C.N.J.C., K.B., S.H., M.C., M.R., J.L.B.), the National Institute for Health Research (NIHR) Health Protection Research Unit in Vaccines and Immunisation, London School of Hygiene and Tropical Medicine (N.A., G.A., C.N.J.C., K.B., M.R., J.L.B.), the Paediatric Infectious Diseases Research Group, St. George's University of London (R.M., S.N.L.), the Medical Research Council Centre for Global Infectious Disease Analysis (N.F.) and the NIHR Health Protection Research Unit in Respiratory Infections (N.F., M.Z., J.L.B.), Imperial College London, and Guy's and St. Thomas's Hospital NHS Trust (M.C.), London, Wellcome Sanger Institute, Hinxton (J.C.B.), and Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford (S.H.) - all in the United Kingdom
| | - Paula B Blomquist
- From the U.K. Health Security Agency (N.A., J.S., F.K., S. Toffa, T.R., E.G., C.G., M.K., N.G., A.-M.O., D.S., P.B.B., A.Z., S.N., N.I.B.A.A., S. Thelwall, G.D., R.M., G.A., S.G., R.E., S.N.L., M.Z., C.N.J.C., K.B., S.H., M.C., M.R., J.L.B.), the National Institute for Health Research (NIHR) Health Protection Research Unit in Vaccines and Immunisation, London School of Hygiene and Tropical Medicine (N.A., G.A., C.N.J.C., K.B., M.R., J.L.B.), the Paediatric Infectious Diseases Research Group, St. George's University of London (R.M., S.N.L.), the Medical Research Council Centre for Global Infectious Disease Analysis (N.F.) and the NIHR Health Protection Research Unit in Respiratory Infections (N.F., M.Z., J.L.B.), Imperial College London, and Guy's and St. Thomas's Hospital NHS Trust (M.C.), London, Wellcome Sanger Institute, Hinxton (J.C.B.), and Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford (S.H.) - all in the United Kingdom
| | - Asad Zaidi
- From the U.K. Health Security Agency (N.A., J.S., F.K., S. Toffa, T.R., E.G., C.G., M.K., N.G., A.-M.O., D.S., P.B.B., A.Z., S.N., N.I.B.A.A., S. Thelwall, G.D., R.M., G.A., S.G., R.E., S.N.L., M.Z., C.N.J.C., K.B., S.H., M.C., M.R., J.L.B.), the National Institute for Health Research (NIHR) Health Protection Research Unit in Vaccines and Immunisation, London School of Hygiene and Tropical Medicine (N.A., G.A., C.N.J.C., K.B., M.R., J.L.B.), the Paediatric Infectious Diseases Research Group, St. George's University of London (R.M., S.N.L.), the Medical Research Council Centre for Global Infectious Disease Analysis (N.F.) and the NIHR Health Protection Research Unit in Respiratory Infections (N.F., M.Z., J.L.B.), Imperial College London, and Guy's and St. Thomas's Hospital NHS Trust (M.C.), London, Wellcome Sanger Institute, Hinxton (J.C.B.), and Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford (S.H.) - all in the United Kingdom
| | - Sophie Nash
- From the U.K. Health Security Agency (N.A., J.S., F.K., S. Toffa, T.R., E.G., C.G., M.K., N.G., A.-M.O., D.S., P.B.B., A.Z., S.N., N.I.B.A.A., S. Thelwall, G.D., R.M., G.A., S.G., R.E., S.N.L., M.Z., C.N.J.C., K.B., S.H., M.C., M.R., J.L.B.), the National Institute for Health Research (NIHR) Health Protection Research Unit in Vaccines and Immunisation, London School of Hygiene and Tropical Medicine (N.A., G.A., C.N.J.C., K.B., M.R., J.L.B.), the Paediatric Infectious Diseases Research Group, St. George's University of London (R.M., S.N.L.), the Medical Research Council Centre for Global Infectious Disease Analysis (N.F.) and the NIHR Health Protection Research Unit in Respiratory Infections (N.F., M.Z., J.L.B.), Imperial College London, and Guy's and St. Thomas's Hospital NHS Trust (M.C.), London, Wellcome Sanger Institute, Hinxton (J.C.B.), and Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford (S.H.) - all in the United Kingdom
| | - Nurin Iwani Binti Abdul Aziz
- From the U.K. Health Security Agency (N.A., J.S., F.K., S. Toffa, T.R., E.G., C.G., M.K., N.G., A.-M.O., D.S., P.B.B., A.Z., S.N., N.I.B.A.A., S. Thelwall, G.D., R.M., G.A., S.G., R.E., S.N.L., M.Z., C.N.J.C., K.B., S.H., M.C., M.R., J.L.B.), the National Institute for Health Research (NIHR) Health Protection Research Unit in Vaccines and Immunisation, London School of Hygiene and Tropical Medicine (N.A., G.A., C.N.J.C., K.B., M.R., J.L.B.), the Paediatric Infectious Diseases Research Group, St. George's University of London (R.M., S.N.L.), the Medical Research Council Centre for Global Infectious Disease Analysis (N.F.) and the NIHR Health Protection Research Unit in Respiratory Infections (N.F., M.Z., J.L.B.), Imperial College London, and Guy's and St. Thomas's Hospital NHS Trust (M.C.), London, Wellcome Sanger Institute, Hinxton (J.C.B.), and Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford (S.H.) - all in the United Kingdom
| | - Simon Thelwall
- From the U.K. Health Security Agency (N.A., J.S., F.K., S. Toffa, T.R., E.G., C.G., M.K., N.G., A.-M.O., D.S., P.B.B., A.Z., S.N., N.I.B.A.A., S. Thelwall, G.D., R.M., G.A., S.G., R.E., S.N.L., M.Z., C.N.J.C., K.B., S.H., M.C., M.R., J.L.B.), the National Institute for Health Research (NIHR) Health Protection Research Unit in Vaccines and Immunisation, London School of Hygiene and Tropical Medicine (N.A., G.A., C.N.J.C., K.B., M.R., J.L.B.), the Paediatric Infectious Diseases Research Group, St. George's University of London (R.M., S.N.L.), the Medical Research Council Centre for Global Infectious Disease Analysis (N.F.) and the NIHR Health Protection Research Unit in Respiratory Infections (N.F., M.Z., J.L.B.), Imperial College London, and Guy's and St. Thomas's Hospital NHS Trust (M.C.), London, Wellcome Sanger Institute, Hinxton (J.C.B.), and Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford (S.H.) - all in the United Kingdom
| | - Gavin Dabrera
- From the U.K. Health Security Agency (N.A., J.S., F.K., S. Toffa, T.R., E.G., C.G., M.K., N.G., A.-M.O., D.S., P.B.B., A.Z., S.N., N.I.B.A.A., S. Thelwall, G.D., R.M., G.A., S.G., R.E., S.N.L., M.Z., C.N.J.C., K.B., S.H., M.C., M.R., J.L.B.), the National Institute for Health Research (NIHR) Health Protection Research Unit in Vaccines and Immunisation, London School of Hygiene and Tropical Medicine (N.A., G.A., C.N.J.C., K.B., M.R., J.L.B.), the Paediatric Infectious Diseases Research Group, St. George's University of London (R.M., S.N.L.), the Medical Research Council Centre for Global Infectious Disease Analysis (N.F.) and the NIHR Health Protection Research Unit in Respiratory Infections (N.F., M.Z., J.L.B.), Imperial College London, and Guy's and St. Thomas's Hospital NHS Trust (M.C.), London, Wellcome Sanger Institute, Hinxton (J.C.B.), and Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford (S.H.) - all in the United Kingdom
| | - Richard Myers
- From the U.K. Health Security Agency (N.A., J.S., F.K., S. Toffa, T.R., E.G., C.G., M.K., N.G., A.-M.O., D.S., P.B.B., A.Z., S.N., N.I.B.A.A., S. Thelwall, G.D., R.M., G.A., S.G., R.E., S.N.L., M.Z., C.N.J.C., K.B., S.H., M.C., M.R., J.L.B.), the National Institute for Health Research (NIHR) Health Protection Research Unit in Vaccines and Immunisation, London School of Hygiene and Tropical Medicine (N.A., G.A., C.N.J.C., K.B., M.R., J.L.B.), the Paediatric Infectious Diseases Research Group, St. George's University of London (R.M., S.N.L.), the Medical Research Council Centre for Global Infectious Disease Analysis (N.F.) and the NIHR Health Protection Research Unit in Respiratory Infections (N.F., M.Z., J.L.B.), Imperial College London, and Guy's and St. Thomas's Hospital NHS Trust (M.C.), London, Wellcome Sanger Institute, Hinxton (J.C.B.), and Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford (S.H.) - all in the United Kingdom
| | - Gayatri Amirthalingam
- From the U.K. Health Security Agency (N.A., J.S., F.K., S. Toffa, T.R., E.G., C.G., M.K., N.G., A.-M.O., D.S., P.B.B., A.Z., S.N., N.I.B.A.A., S. Thelwall, G.D., R.M., G.A., S.G., R.E., S.N.L., M.Z., C.N.J.C., K.B., S.H., M.C., M.R., J.L.B.), the National Institute for Health Research (NIHR) Health Protection Research Unit in Vaccines and Immunisation, London School of Hygiene and Tropical Medicine (N.A., G.A., C.N.J.C., K.B., M.R., J.L.B.), the Paediatric Infectious Diseases Research Group, St. George's University of London (R.M., S.N.L.), the Medical Research Council Centre for Global Infectious Disease Analysis (N.F.) and the NIHR Health Protection Research Unit in Respiratory Infections (N.F., M.Z., J.L.B.), Imperial College London, and Guy's and St. Thomas's Hospital NHS Trust (M.C.), London, Wellcome Sanger Institute, Hinxton (J.C.B.), and Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford (S.H.) - all in the United Kingdom
| | - Saheer Gharbia
- From the U.K. Health Security Agency (N.A., J.S., F.K., S. Toffa, T.R., E.G., C.G., M.K., N.G., A.-M.O., D.S., P.B.B., A.Z., S.N., N.I.B.A.A., S. Thelwall, G.D., R.M., G.A., S.G., R.E., S.N.L., M.Z., C.N.J.C., K.B., S.H., M.C., M.R., J.L.B.), the National Institute for Health Research (NIHR) Health Protection Research Unit in Vaccines and Immunisation, London School of Hygiene and Tropical Medicine (N.A., G.A., C.N.J.C., K.B., M.R., J.L.B.), the Paediatric Infectious Diseases Research Group, St. George's University of London (R.M., S.N.L.), the Medical Research Council Centre for Global Infectious Disease Analysis (N.F.) and the NIHR Health Protection Research Unit in Respiratory Infections (N.F., M.Z., J.L.B.), Imperial College London, and Guy's and St. Thomas's Hospital NHS Trust (M.C.), London, Wellcome Sanger Institute, Hinxton (J.C.B.), and Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford (S.H.) - all in the United Kingdom
| | - Jeffrey C Barrett
- From the U.K. Health Security Agency (N.A., J.S., F.K., S. Toffa, T.R., E.G., C.G., M.K., N.G., A.-M.O., D.S., P.B.B., A.Z., S.N., N.I.B.A.A., S. Thelwall, G.D., R.M., G.A., S.G., R.E., S.N.L., M.Z., C.N.J.C., K.B., S.H., M.C., M.R., J.L.B.), the National Institute for Health Research (NIHR) Health Protection Research Unit in Vaccines and Immunisation, London School of Hygiene and Tropical Medicine (N.A., G.A., C.N.J.C., K.B., M.R., J.L.B.), the Paediatric Infectious Diseases Research Group, St. George's University of London (R.M., S.N.L.), the Medical Research Council Centre for Global Infectious Disease Analysis (N.F.) and the NIHR Health Protection Research Unit in Respiratory Infections (N.F., M.Z., J.L.B.), Imperial College London, and Guy's and St. Thomas's Hospital NHS Trust (M.C.), London, Wellcome Sanger Institute, Hinxton (J.C.B.), and Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford (S.H.) - all in the United Kingdom
| | - Richard Elson
- From the U.K. Health Security Agency (N.A., J.S., F.K., S. Toffa, T.R., E.G., C.G., M.K., N.G., A.-M.O., D.S., P.B.B., A.Z., S.N., N.I.B.A.A., S. Thelwall, G.D., R.M., G.A., S.G., R.E., S.N.L., M.Z., C.N.J.C., K.B., S.H., M.C., M.R., J.L.B.), the National Institute for Health Research (NIHR) Health Protection Research Unit in Vaccines and Immunisation, London School of Hygiene and Tropical Medicine (N.A., G.A., C.N.J.C., K.B., M.R., J.L.B.), the Paediatric Infectious Diseases Research Group, St. George's University of London (R.M., S.N.L.), the Medical Research Council Centre for Global Infectious Disease Analysis (N.F.) and the NIHR Health Protection Research Unit in Respiratory Infections (N.F., M.Z., J.L.B.), Imperial College London, and Guy's and St. Thomas's Hospital NHS Trust (M.C.), London, Wellcome Sanger Institute, Hinxton (J.C.B.), and Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford (S.H.) - all in the United Kingdom
| | - Shamez N Ladhani
- From the U.K. Health Security Agency (N.A., J.S., F.K., S. Toffa, T.R., E.G., C.G., M.K., N.G., A.-M.O., D.S., P.B.B., A.Z., S.N., N.I.B.A.A., S. Thelwall, G.D., R.M., G.A., S.G., R.E., S.N.L., M.Z., C.N.J.C., K.B., S.H., M.C., M.R., J.L.B.), the National Institute for Health Research (NIHR) Health Protection Research Unit in Vaccines and Immunisation, London School of Hygiene and Tropical Medicine (N.A., G.A., C.N.J.C., K.B., M.R., J.L.B.), the Paediatric Infectious Diseases Research Group, St. George's University of London (R.M., S.N.L.), the Medical Research Council Centre for Global Infectious Disease Analysis (N.F.) and the NIHR Health Protection Research Unit in Respiratory Infections (N.F., M.Z., J.L.B.), Imperial College London, and Guy's and St. Thomas's Hospital NHS Trust (M.C.), London, Wellcome Sanger Institute, Hinxton (J.C.B.), and Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford (S.H.) - all in the United Kingdom
| | - Neil Ferguson
- From the U.K. Health Security Agency (N.A., J.S., F.K., S. Toffa, T.R., E.G., C.G., M.K., N.G., A.-M.O., D.S., P.B.B., A.Z., S.N., N.I.B.A.A., S. Thelwall, G.D., R.M., G.A., S.G., R.E., S.N.L., M.Z., C.N.J.C., K.B., S.H., M.C., M.R., J.L.B.), the National Institute for Health Research (NIHR) Health Protection Research Unit in Vaccines and Immunisation, London School of Hygiene and Tropical Medicine (N.A., G.A., C.N.J.C., K.B., M.R., J.L.B.), the Paediatric Infectious Diseases Research Group, St. George's University of London (R.M., S.N.L.), the Medical Research Council Centre for Global Infectious Disease Analysis (N.F.) and the NIHR Health Protection Research Unit in Respiratory Infections (N.F., M.Z., J.L.B.), Imperial College London, and Guy's and St. Thomas's Hospital NHS Trust (M.C.), London, Wellcome Sanger Institute, Hinxton (J.C.B.), and Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford (S.H.) - all in the United Kingdom
| | - Maria Zambon
- From the U.K. Health Security Agency (N.A., J.S., F.K., S. Toffa, T.R., E.G., C.G., M.K., N.G., A.-M.O., D.S., P.B.B., A.Z., S.N., N.I.B.A.A., S. Thelwall, G.D., R.M., G.A., S.G., R.E., S.N.L., M.Z., C.N.J.C., K.B., S.H., M.C., M.R., J.L.B.), the National Institute for Health Research (NIHR) Health Protection Research Unit in Vaccines and Immunisation, London School of Hygiene and Tropical Medicine (N.A., G.A., C.N.J.C., K.B., M.R., J.L.B.), the Paediatric Infectious Diseases Research Group, St. George's University of London (R.M., S.N.L.), the Medical Research Council Centre for Global Infectious Disease Analysis (N.F.) and the NIHR Health Protection Research Unit in Respiratory Infections (N.F., M.Z., J.L.B.), Imperial College London, and Guy's and St. Thomas's Hospital NHS Trust (M.C.), London, Wellcome Sanger Institute, Hinxton (J.C.B.), and Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford (S.H.) - all in the United Kingdom
| | - Colin N J Campbell
- From the U.K. Health Security Agency (N.A., J.S., F.K., S. Toffa, T.R., E.G., C.G., M.K., N.G., A.-M.O., D.S., P.B.B., A.Z., S.N., N.I.B.A.A., S. Thelwall, G.D., R.M., G.A., S.G., R.E., S.N.L., M.Z., C.N.J.C., K.B., S.H., M.C., M.R., J.L.B.), the National Institute for Health Research (NIHR) Health Protection Research Unit in Vaccines and Immunisation, London School of Hygiene and Tropical Medicine (N.A., G.A., C.N.J.C., K.B., M.R., J.L.B.), the Paediatric Infectious Diseases Research Group, St. George's University of London (R.M., S.N.L.), the Medical Research Council Centre for Global Infectious Disease Analysis (N.F.) and the NIHR Health Protection Research Unit in Respiratory Infections (N.F., M.Z., J.L.B.), Imperial College London, and Guy's and St. Thomas's Hospital NHS Trust (M.C.), London, Wellcome Sanger Institute, Hinxton (J.C.B.), and Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford (S.H.) - all in the United Kingdom
| | - Kevin Brown
- From the U.K. Health Security Agency (N.A., J.S., F.K., S. Toffa, T.R., E.G., C.G., M.K., N.G., A.-M.O., D.S., P.B.B., A.Z., S.N., N.I.B.A.A., S. Thelwall, G.D., R.M., G.A., S.G., R.E., S.N.L., M.Z., C.N.J.C., K.B., S.H., M.C., M.R., J.L.B.), the National Institute for Health Research (NIHR) Health Protection Research Unit in Vaccines and Immunisation, London School of Hygiene and Tropical Medicine (N.A., G.A., C.N.J.C., K.B., M.R., J.L.B.), the Paediatric Infectious Diseases Research Group, St. George's University of London (R.M., S.N.L.), the Medical Research Council Centre for Global Infectious Disease Analysis (N.F.) and the NIHR Health Protection Research Unit in Respiratory Infections (N.F., M.Z., J.L.B.), Imperial College London, and Guy's and St. Thomas's Hospital NHS Trust (M.C.), London, Wellcome Sanger Institute, Hinxton (J.C.B.), and Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford (S.H.) - all in the United Kingdom
| | - Susan Hopkins
- From the U.K. Health Security Agency (N.A., J.S., F.K., S. Toffa, T.R., E.G., C.G., M.K., N.G., A.-M.O., D.S., P.B.B., A.Z., S.N., N.I.B.A.A., S. Thelwall, G.D., R.M., G.A., S.G., R.E., S.N.L., M.Z., C.N.J.C., K.B., S.H., M.C., M.R., J.L.B.), the National Institute for Health Research (NIHR) Health Protection Research Unit in Vaccines and Immunisation, London School of Hygiene and Tropical Medicine (N.A., G.A., C.N.J.C., K.B., M.R., J.L.B.), the Paediatric Infectious Diseases Research Group, St. George's University of London (R.M., S.N.L.), the Medical Research Council Centre for Global Infectious Disease Analysis (N.F.) and the NIHR Health Protection Research Unit in Respiratory Infections (N.F., M.Z., J.L.B.), Imperial College London, and Guy's and St. Thomas's Hospital NHS Trust (M.C.), London, Wellcome Sanger Institute, Hinxton (J.C.B.), and Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford (S.H.) - all in the United Kingdom
| | - Meera Chand
- From the U.K. Health Security Agency (N.A., J.S., F.K., S. Toffa, T.R., E.G., C.G., M.K., N.G., A.-M.O., D.S., P.B.B., A.Z., S.N., N.I.B.A.A., S. Thelwall, G.D., R.M., G.A., S.G., R.E., S.N.L., M.Z., C.N.J.C., K.B., S.H., M.C., M.R., J.L.B.), the National Institute for Health Research (NIHR) Health Protection Research Unit in Vaccines and Immunisation, London School of Hygiene and Tropical Medicine (N.A., G.A., C.N.J.C., K.B., M.R., J.L.B.), the Paediatric Infectious Diseases Research Group, St. George's University of London (R.M., S.N.L.), the Medical Research Council Centre for Global Infectious Disease Analysis (N.F.) and the NIHR Health Protection Research Unit in Respiratory Infections (N.F., M.Z., J.L.B.), Imperial College London, and Guy's and St. Thomas's Hospital NHS Trust (M.C.), London, Wellcome Sanger Institute, Hinxton (J.C.B.), and Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford (S.H.) - all in the United Kingdom
| | - Mary Ramsay
- From the U.K. Health Security Agency (N.A., J.S., F.K., S. Toffa, T.R., E.G., C.G., M.K., N.G., A.-M.O., D.S., P.B.B., A.Z., S.N., N.I.B.A.A., S. Thelwall, G.D., R.M., G.A., S.G., R.E., S.N.L., M.Z., C.N.J.C., K.B., S.H., M.C., M.R., J.L.B.), the National Institute for Health Research (NIHR) Health Protection Research Unit in Vaccines and Immunisation, London School of Hygiene and Tropical Medicine (N.A., G.A., C.N.J.C., K.B., M.R., J.L.B.), the Paediatric Infectious Diseases Research Group, St. George's University of London (R.M., S.N.L.), the Medical Research Council Centre for Global Infectious Disease Analysis (N.F.) and the NIHR Health Protection Research Unit in Respiratory Infections (N.F., M.Z., J.L.B.), Imperial College London, and Guy's and St. Thomas's Hospital NHS Trust (M.C.), London, Wellcome Sanger Institute, Hinxton (J.C.B.), and Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford (S.H.) - all in the United Kingdom
| | - Jamie Lopez Bernal
- From the U.K. Health Security Agency (N.A., J.S., F.K., S. Toffa, T.R., E.G., C.G., M.K., N.G., A.-M.O., D.S., P.B.B., A.Z., S.N., N.I.B.A.A., S. Thelwall, G.D., R.M., G.A., S.G., R.E., S.N.L., M.Z., C.N.J.C., K.B., S.H., M.C., M.R., J.L.B.), the National Institute for Health Research (NIHR) Health Protection Research Unit in Vaccines and Immunisation, London School of Hygiene and Tropical Medicine (N.A., G.A., C.N.J.C., K.B., M.R., J.L.B.), the Paediatric Infectious Diseases Research Group, St. George's University of London (R.M., S.N.L.), the Medical Research Council Centre for Global Infectious Disease Analysis (N.F.) and the NIHR Health Protection Research Unit in Respiratory Infections (N.F., M.Z., J.L.B.), Imperial College London, and Guy's and St. Thomas's Hospital NHS Trust (M.C.), London, Wellcome Sanger Institute, Hinxton (J.C.B.), and Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford (S.H.) - all in the United Kingdom
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Brüssow H. COVID-19: Omicron - the latest, the least virulent, but probably not the last variant of concern of SARS-CoV-2. Microb Biotechnol 2022; 15:1927-1939. [PMID: 35443078 PMCID: PMC9111164 DOI: 10.1111/1751-7915.14064] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 04/08/2022] [Indexed: 01/10/2023] Open
Abstract
The Omicron variant rapidly became the dominant SARS‐CoV‐2 strain in South Africa and elsewhere. This review explores whether this rise was due to an increased transmission of the variant or its escape from population immunity by an extensively mutated spike protein. The mutations affected the structure of the spike protein leading to the loss of neutralization by most, but not all, therapeutic monoclonal antibodies. Omicron also shows substantial immune escape from serum antibodies in convalescent patients and vaccinees. A booster immunization increased, however, the titre and breadth of antiviral antibody response. The cellular immune response against Omicron was largely preserved explaining a satisfying protection of boosted vaccinees against severe infections. Clinicians observed less severe infection with Omicron, but other scientists warned that this must not necessarily reflect less intrinsic virulence. However, in animal experiments with mice and hamsters, Omicron infections also displayed a lesser virulence than previous VOCs and lung functions were less compromised. Cell biologists demonstrated that Omicron differs from Delta by preferring the endocytic pathway for cell entry over fusion with the plasma membrane which might explain Omicron’s distinct replication along the respiratory tract compared with Delta. Omicron represents a distinct evolutionary lineage that deviated from the mainstream of evolving SARS‐CoV‐2 already in mid‐2020 raising questions about where it circulated before getting widespread in December 2021. The role of Omicron for the future trajectory of the COVID‐19 pandemic is discussed. The Omicron variant rapidly became the dominant SARS‐CoV‐2 strain in South Africa and elsewhere. This review explores whether this rise was due to an increased transmission of the variant or its escape from population immunity by an extensively mutated spike protein. Clinicians observed less severe infection with Omicron, but other scientists warned that this must not necessarily reflect less intrinsic virulence.
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Affiliation(s)
- Harald Brüssow
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium
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585
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Mazzotta V, Cozzi-Lepri A, Colavita F, Lanini S, Rosati S, Lalle E, Mastrorosa I, Cimaglia C, Vergori A, Bevilacqua N, Lapa D, Mariano A, Bettini A, Agrati C, Piselli P, Girardi E, Castilletti C, Garbuglia AR, Vaia F, Nicastri E, Antinori A. Emulation of a Target Trial From Observational Data to Compare Effectiveness of Casirivimab/Imdevimab and Bamlanivimab/Etesevimab for Early Treatment of Non-Hospitalized Patients With COVID-19. Front Immunol 2022; 13:868020. [PMID: 35514955 PMCID: PMC9066636 DOI: 10.3389/fimmu.2022.868020] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/24/2022] [Indexed: 11/22/2022] Open
Abstract
Objectives Comparative analysis between different monoclonal antibodies (mAbs) against SARS-CoV-2 are lacking. We present an emulation trial from observational data to compare effectiveness of Bamlanivimab/Etesevimab (BAM/ETE) and Casirivimab/Imdevimab (CAS/IMD) in outpatients with early mild-to-moderate COVID-19 in a real-world scenario of variants of concern (VoCs) from Alpha to Delta. Methods Allocation to treatment was subject to mAbs availability, and the measured factors were not used to determine which combination to use. Patients were followed through day 30. Viral load was measured by cycle threshold (CT) on D1 (baseline) and D7.Primary outcome was time to COVID-19-related hospitalization or death from any cause over days 0-30. Weighted pooled logistic regression and marginal structural Cox model by inverse probability weights were used to compare BAM/ETE vs. CAS/IMD. ANCOVA was used to compare mean D7 CT values by intervention. Models were adjusted for calendar month, MASS score and VoCs. We evaluated effect measure modification by VoCs, vaccination, D1 CT levels and enrolment period. Results COVID19-related hospitalization or death from any cause occurred in 15 of 237 patients in the BAM/ETE group (6.3%) and in 4 of 196 patients in the CAS/IMD group (2.0%) (relative risk reduction [1 minus the relative risk] 72%; p=0.024). Subset analysis carried no evidence that the effect of the intervention was different across stratification factors. There was no evidence in viral load reduction from baseline through day 7 across the two groups (+0.17, 95% -1.41;+1.74, p=0.83). Among patients who experienced primary outcome, none showed a negative RT-PCR test in nasopharyngeal swab (p=0.009) and 82.4% showed still high viral load (p<0.001) on D7. Conclusions In a pre-Omicron epidemiologic scenario, CAS/IMD reduced risk of clinical progression of COVID-19 compared to BAM/ETE. This effect was not associated with a concomitant difference in virological response.
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Affiliation(s)
- Valentina Mazzotta
- Clinical and Infectious Diseases Research Department, National Institute for Infectious Diseases Lazzaro Spallanzani Istituiti di Ricovero e Cura a Carattere Scientifico (IRCCS), Roma, Italy
| | - Alessandro Cozzi-Lepri
- Centre for Clinical Research, Epidemiology, Modelling and Evaluation (CREME), Institute for Global Health, University College London (UCL), London, United Kingdom
| | - Francesca Colavita
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani Istituiti di Ricovero e Cura a Carattere Scientifico (IRCCS), Roma, Italy
| | - Simone Lanini
- Clinical and Infectious Diseases Research Department, National Institute for Infectious Diseases Lazzaro Spallanzani Istituiti di Ricovero e Cura a Carattere Scientifico (IRCCS), Roma, Italy
| | - Silvia Rosati
- Clinical and Infectious Diseases Research Department, National Institute for Infectious Diseases Lazzaro Spallanzani Istituiti di Ricovero e Cura a Carattere Scientifico (IRCCS), Roma, Italy
| | - Eleonora Lalle
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani Istituiti di Ricovero e Cura a Carattere Scientifico (IRCCS), Roma, Italy
| | - Ilaria Mastrorosa
- Clinical and Infectious Diseases Research Department, National Institute for Infectious Diseases Lazzaro Spallanzani Istituiti di Ricovero e Cura a Carattere Scientifico (IRCCS), Roma, Italy
| | - Claudia Cimaglia
- Clinical Epidemiology, National Institute for Infectious Diseases Lazzaro Spallanzani Istituiti di Ricovero e Cura a Carattere Scientifico (IRCCS), Roma, Italy
| | - Alessandra Vergori
- Clinical and Infectious Diseases Research Department, National Institute for Infectious Diseases Lazzaro Spallanzani Istituiti di Ricovero e Cura a Carattere Scientifico (IRCCS), Roma, Italy
| | - Nazario Bevilacqua
- Clinical and Infectious Diseases Research Department, National Institute for Infectious Diseases Lazzaro Spallanzani Istituiti di Ricovero e Cura a Carattere Scientifico (IRCCS), Roma, Italy
| | - Daniele Lapa
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani Istituiti di Ricovero e Cura a Carattere Scientifico (IRCCS), Roma, Italy
| | - Andrea Mariano
- Clinical and Infectious Diseases Research Department, National Institute for Infectious Diseases Lazzaro Spallanzani Istituiti di Ricovero e Cura a Carattere Scientifico (IRCCS), Roma, Italy
| | - Aurora Bettini
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani Istituiti di Ricovero e Cura a Carattere Scientifico (IRCCS), Roma, Italy
| | - Chiara Agrati
- Laboratory of Cellular Immunology and Pharmacology, National Institute for Infectious Diseases Lazzaro Spallanzani Istituiti di Ricovero e Cura a Carattere Scientifico (IRCCS), Roma, Italy
| | - Pierluca Piselli
- Clinical Epidemiology, National Institute for Infectious Diseases Lazzaro Spallanzani Istituiti di Ricovero e Cura a Carattere Scientifico (IRCCS), Roma, Italy
| | - Enrico Girardi
- Scientific Direction, National Institute for Infectious Diseases Lazzaro Spallanzani Istituiti di Ricovero e Cura a Carattere Scientifico (IRCCS), Roma, Italy
| | - Concetta Castilletti
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani Istituiti di Ricovero e Cura a Carattere Scientifico (IRCCS), Roma, Italy
| | - Anna Rosa Garbuglia
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani Istituiti di Ricovero e Cura a Carattere Scientifico (IRCCS), Roma, Italy
| | - Francesco Vaia
- Health Direction, National Institute for Infectious Diseases Lazzaro Spallanzani Istituiti di Ricovero e Cura a Carattere Scientifico (IRCCS), Roma, Italy
| | - Emanuele Nicastri
- Clinical and Infectious Diseases Research Department, National Institute for Infectious Diseases Lazzaro Spallanzani Istituiti di Ricovero e Cura a Carattere Scientifico (IRCCS), Roma, Italy
| | - Andrea Antinori
- Clinical and Infectious Diseases Research Department, National Institute for Infectious Diseases Lazzaro Spallanzani Istituiti di Ricovero e Cura a Carattere Scientifico (IRCCS), Roma, Italy
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586
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Subramoney K, Mtileni N, Bharuthram A, Davis A, Kalenga B, Rikhotso M, Maphahlele M, Giandhari J, Naidoo Y, Pillay S, Ramphal U, Ramphal Y, Tegally H, Wilkinson E, Mohale T, Ismail A, Mashishi B, Mbenenge N, de Oliveira T, Makatini Z, Fielding BC, Treurnicht FK. Identification of SARS-CoV-2 Omicron variant using spike gene target failure and genotyping assays, Gauteng, South Africa, 2021. J Med Virol 2022; 94:3676-3684. [PMID: 35441368 PMCID: PMC9088381 DOI: 10.1002/jmv.27797] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/06/2022] [Accepted: 04/09/2022] [Indexed: 11/09/2022]
Abstract
The circulation of Omicron BA.1 led to the rapid increase in severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) cases in South Africa in November 2021, which warranted the use of more rapid detection methods. We, therefore, assessed the ability to detect Omicron BA.1 using genotyping assays to identify specific mutations in SARS‐CoV‐2 positive samples, Gauteng province, South Africa. The TaqPath™ COVID‐19 real‐time polymerase chain reaction assay was performed on all samples selected to identify spike gene target failure (SGTF). SARS‐CoV‐2 genotyping assays were used for the detection of del69/70 and K417N mutation. Whole‐genome sequencing was performed on a subset of genotyped samples to confirm these findings. Of the positive samples received, 11.0% (175/1589) were randomly selected to assess if SGTF and genotyping assays, that detect del69/70 and K417N mutations, could identify Omicron BA.1. We identified SGTF in 98.9% (173/175) of samples, of which 88.0% (154/175) had both the del69/70 and K417N mutation. The genotyped samples (45.7%; 80/175) that were sequenced confirmed Omicron BA.1 (97.5%; 78/80). Our data show that genotyping for the detection of the del69/70 and K417N coupled with SGTF is efficient to exclude Alpha and Beta variants and rapidly detect Omicron BA.1. However, we still require assays for the detection of unique mutations that will allow for the differentiation between other Omicron sublineages. Therefore, the use of genotyping assays to detect new dominant or emerging lineages of SARS‐CoV‐2 will be beneficial in limited‐resource settings.
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Affiliation(s)
- Kathleen Subramoney
- Department of Virology, National Health Laboratory Service, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa.,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nkhensani Mtileni
- Department of Virology, National Health Laboratory Service, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
| | - Avani Bharuthram
- Department of Virology, National Health Laboratory Service, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa.,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Ashlyn Davis
- Department of Virology, National Health Laboratory Service, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
| | - Beauty Kalenga
- Department of Virology, National Health Laboratory Service, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
| | - Mikateko Rikhotso
- Department of Virology, National Health Laboratory Service, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
| | - Mpho Maphahlele
- Department of Virology, National Health Laboratory Service, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
| | | | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Yeshnee Naidoo
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Upasana Ramphal
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Yajna Ramphal
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Houriyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Eduan Wilkinson
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Thabo Mohale
- National Institute for Communicable Diseases, Sequencing Core Facility, Johannesburg, South Africa
| | - Arshad Ismail
- National Institute for Communicable Diseases, Sequencing Core Facility, Johannesburg, South Africa
| | - Bonolo Mashishi
- Department of Virology, National Health Laboratory Service, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa.,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nonhlanhla Mbenenge
- Department of Virology, National Health Laboratory Service, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa.,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.,Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Zinhle Makatini
- Department of Virology, National Health Laboratory Service, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa.,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Burtram C Fielding
- Molecular Biology and Virology Research Laboratory, Department of Medical Biosciences, University of the Western Cape, Bellville, South Africa
| | - Florette K Treurnicht
- Department of Virology, National Health Laboratory Service, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa.,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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587
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Liu JZ, Lv HC, Fu YJ, Cui Q. Amomum tsao-ko essential oil, a Novel Anti-COVID-19 Omircon Spike Protein Natural Products: A Computational Study. ARAB J CHEM 2022; 15:103916. [PMID: 35462797 PMCID: PMC9014638 DOI: 10.1016/j.arabjc.2022.103916] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 04/10/2022] [Indexed: 12/20/2022] Open
Abstract
Since the outbreak of COVID-19, this virus has been constantly mutating. The latest mutant Omicron has been identified as VOC by WHO. The main reason for its concern is the mutation of 46 amino acids in spike protein, which has brought the global epidemic prevention into another difficulty. Herbal aromatic plant Amomum tsao-ko was excavated from formula 1 and 2 for the treatment of COVID-19 in China, and its active components were extracted and identified. Molecular dynamics simulation and Fpocket were applied to find the key sites on RBDOmicron, and molecular docking was also used to reveal the interaction between A. tsao-ko essential oil (AEO) and RBDOmicron. The AEO components were analyzed and identified by GC/Q-TOF MS. There were 20 kinds of AEO with a relative area percentage of more than 1%, and they were related to the three active centres of RBDOmicron. In this study, virtual screening was used to mine the essential oil components of medicinal plants, and it was found that the components could interact with the spike protein RBD in aerosol to block the interaction of RBD and hACE2, thus cutting off the transmission route and protecting the host. This study has certain guiding significance in the modernization of Traditional Chinese medicine and the prevention of COVID-19.
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Affiliation(s)
- Ju-Zhao Liu
- College of Pharmaceutical Science, Zhejiang Chinese Medical University, Hangzhou 311402, PR China
| | - Hong-Chang Lv
- School of Modern Post (School of Automation), Beijing University of Posts and Telecommunications, Beijing 100876, China
| | - Yu-Jie Fu
- College of Forestry, Beijing Forestry University, No. 35, Tsinghua East Road, Haidian District, Beijing 100083, PR China
| | - Qi Cui
- College of Pharmaceutical Science, Zhejiang Chinese Medical University, Hangzhou 311402, PR China
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588
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Pandit P, Bhatt P, Sahay RR, Joshi Y, Patil DY, Yadav PD. A case of breakthrough infection with SARS-CoV-2 Delta derivative and reinfection with Omicron variant in a fully vaccinated health care professional. J Infect 2022; 85:e15-e17. [PMID: 35447232 PMCID: PMC9014656 DOI: 10.1016/j.jinf.2022.04.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 04/10/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Priyanka Pandit
- Indian Council of Medical Research-National Institute of Virology, Pune, India Pin-411021
| | - Puneet Bhatt
- Army Hospital Research and Referral, New Delhi, India Pin-110010
| | - Rima R Sahay
- Indian Council of Medical Research-National Institute of Virology, Pune, India Pin-411021
| | - Yash Joshi
- Indian Council of Medical Research-National Institute of Virology, Pune, India Pin-411021
| | - Deepak Y Patil
- Indian Council of Medical Research-National Institute of Virology, Pune, India Pin-411021
| | - Pragya D Yadav
- Indian Council of Medical Research-National Institute of Virology, Pune, India Pin-411021.
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589
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Verkhivker G, Agajanian S, Kassab R, Krishnan K. Computer Simulations and Network-Based Profiling of Binding and Allosteric Interactions of SARS-CoV-2 Spike Variant Complexes and the Host Receptor: Dissecting the Mechanistic Effects of the Delta and Omicron Mutations. Int J Mol Sci 2022; 23:4376. [PMID: 35457196 PMCID: PMC9032413 DOI: 10.3390/ijms23084376] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/12/2022] [Accepted: 04/14/2022] [Indexed: 02/01/2023] Open
Abstract
In this study, we combine all-atom MD simulations and comprehensive mutational scanning of S-RBD complexes with the angiotensin-converting enzyme 2 (ACE2) host receptor in the native form as well as the S-RBD Delta and Omicron variants to (a) examine the differences in the dynamic signatures of the S-RBD complexes and (b) identify the critical binding hotspots and sensitivity of the mutational positions. We also examined the differences in allosteric interactions and communications in the S-RBD complexes for the Delta and Omicron variants. Through the perturbation-based scanning of the allosteric propensities of the SARS-CoV-2 S-RBD residues and dynamics-based network centrality and community analyses, we characterize the global mediating centers in the complexes and the nature of local stabilizing communities. We show that a constellation of mutational sites (G496S, Q498R, N501Y and Y505H) correspond to key binding energy hotspots and also contribute decisively to the key interfacial communities that mediate allosteric communications between S-RBD and ACE2. These Omicron mutations are responsible for both favorable local binding interactions and long-range allosteric interactions, providing key functional centers that mediate the high transmissibility of the virus. At the same time, our results show that other mutational sites could provide a "flexible shield" surrounding the stable community network, thereby allowing the Omicron virus to modulate immune evasion at different epitopes, while protecting the integrity of binding and allosteric interactions in the RBD-ACE2 complexes. This study suggests that the SARS-CoV-2 S protein may exploit the plasticity of the RBD to generate escape mutants, while engaging a small group of functional hotspots to mediate efficient local binding interactions and long-range allosteric communications with ACE2.
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Affiliation(s)
- Gennady Verkhivker
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA; (S.A.); (R.K.); (K.K.)
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, USA
| | - Steve Agajanian
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA; (S.A.); (R.K.); (K.K.)
| | - Ryan Kassab
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA; (S.A.); (R.K.); (K.K.)
| | - Keerthi Krishnan
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA; (S.A.); (R.K.); (K.K.)
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590
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Chekol Abebe E, Tiruneh G/Medhin M, Behaile T/Mariam A, Asmamaw Dejenie T, Mengie Ayele T, Tadele Admasu F, Tilahun Muche Z, Asmare Adela G. Mutational Pattern, Impacts and Potential Preventive Strategies of Omicron SARS-CoV-2 Variant Infection. Infect Drug Resist 2022; 15:1871-1887. [PMID: 35450114 PMCID: PMC9017707 DOI: 10.2147/idr.s360103] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 04/08/2022] [Indexed: 01/18/2023] Open
Abstract
Since the emergence of COVID 19, the authentic SARS-CoV-2 has evolved into a range of novel variants that are of more global concern. In late November 2021, the Omicron (lineage B.1.1.529) variant was identified as a new variant and considered as the fifth variant of concern. Omicron harbors a genetic profile that is exceedingly unusual, with a huge number of mutations. Above thirty mutations are localized in the S protein, while some are found in other structural and non-structural proteins. Half of the mutations in the S protein are in the RBD, which is a major target of antibodies, showing that Omicron mutations may affect antibody binding affinity to the S protein. The Omicron variant has been found to result in immune escape, therapeutic or vaccine escape, as well as increased transmissibility and reinfection risk, explaining its rapid international spread that sparks a global alarm even more serious than the previously reported variants. Omicron has the capability to bypass at least some of the multi-faceted immune responses induced by prior infection or vaccination. It is shown to extensively escape neutralizing antibodies while evading cell mediated immune defense to a lesser extent. The efficacy of COVID 19 vaccines against Omicron variant is decreased with primary vaccination, showing that the vaccine is less efficient in preventing Omicron infections. However, after receiving a booster vaccine dose, the immunological response to Omicron significantly improved and hold promising results. Despite the mild nature of the disease in most vaccinated people, the rapid spread of Omicron, as well as the increased risk of re-infection, poses yet another major public health concern. Therefore, effort should be devoted to maintaining the existing COVID 19 preventive measures as well as developing new vaccination strategies in order to control the fast dissemination of Omicron.
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Affiliation(s)
- Endeshaw Chekol Abebe
- Department of Medical Biochemistry, College of Health Sciences, Debre Tabor University, Debre Tabor, Ethiopia
| | - Markeshaw Tiruneh G/Medhin
- Department of Medical Biochemistry, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Awgichew Behaile T/Mariam
- Department of Medical Biochemistry, College of Health Sciences, Debre Tabor University, Debre Tabor, Ethiopia
| | - Tadesse Asmamaw Dejenie
- Department of Medical Biochemistry, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Teklie Mengie Ayele
- Department of Pharmacy, College of Health Sciences, Debre Tabor University, Debre Tabor, Ethiopia
| | - Fitalew Tadele Admasu
- Department of Medical Biochemistry, College of Health Sciences, Debre Tabor University, Debre Tabor, Ethiopia
| | - Zelalem Tilahun Muche
- Department of Physiology, College of Health Sciences, Debre Tabor University, Debre Tabor, Ethiopia
| | - Getachew Asmare Adela
- Department of Reproductive Health and Nutrition, School of Public Health, Wolaita Sodo University, Wolaita Sodo, Ethiopia
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591
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Ren Z, Nishimura M, Tjan LH, Furukawa K, Kurahashi Y, Sutandhio S, Aoki K, Hasegawa N, Arii J, Uto K, Matsui K, Sato I, Saegusa J, Godai N, Takeshita K, Yamamoto M, Nagashima T, Mori Y. Large-scale serosurveillance of COVID-19 in Japan: Acquisition of neutralizing antibodies for Delta but not for Omicron and requirement of booster vaccination to overcome the Omicron's outbreak. PLoS One 2022; 17:e0266270. [PMID: 35381036 PMCID: PMC8982849 DOI: 10.1371/journal.pone.0266270] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/17/2022] [Indexed: 11/19/2022] Open
Abstract
Continuous appearance of SARS-CoV-2 variants and mass vaccination have been intricately influencing on the COVID-19 situation. To elucidate the current status in Japan, we analyzed totally 2,000 sera in August (n = 1,000) and December (n = 1,000) 2021 collected from individuals who underwent a health check-up. The anti-N seropositive rate were 2.1% and 3.9% in August and December 2021, respectively, demonstrating a Delta variant endemic during that time; it was approximately twofold higher than the rate based on the PCR-based diagnosis. The anti-S seropositive rate was 38.7% in August and it reached 90.8% in December, in concordance with the vaccination rate in Japan. In the December cohort, 78.7% of the sera showed neutralizing activity against the Delta variant, whereas that against the Omicron was much lower at 36.6%. These analyses revealed that effective immunity against the Delta variant was established in December 2021, however, prompt three-dose vaccination is needed to overcome Omicron’s outbreak.
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Affiliation(s)
- Zhenxiao Ren
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Mitsuhiro Nishimura
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Lidya Handayani Tjan
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Koichi Furukawa
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Yukiya Kurahashi
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Silvia Sutandhio
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Kaito Aoki
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Natsumi Hasegawa
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Jun Arii
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Kenichi Uto
- Department of Clinical Laboratory, Kobe University Hospital, Kobe, Hyogo, Japan
| | - Keiji Matsui
- Department of Clinical Laboratory, Kobe University Hospital, Kobe, Hyogo, Japan
| | - Itsuko Sato
- Department of Clinical Laboratory, Kobe University Hospital, Kobe, Hyogo, Japan
| | - Jun Saegusa
- Department of Clinical Laboratory, Kobe University Hospital, Kobe, Hyogo, Japan
| | - Nonoka Godai
- Department of Life Science, Laboratory of Macromolecular Dynamics and X-ray Crystallography, University of Hyogo, Hyogo, Japan
- Advanced Photon Technology Division, Life Science Research Infrastructure Group, RIKEN SPring-8 Center, Hyogo, Japan
| | - Kohei Takeshita
- Advanced Photon Technology Division, Life Science Research Infrastructure Group, RIKEN SPring-8 Center, Hyogo, Japan
| | - Masaki Yamamoto
- Department of Life Science, Laboratory of Macromolecular Dynamics and X-ray Crystallography, University of Hyogo, Hyogo, Japan
- Advanced Photon Technology Division, Life Science Research Infrastructure Group, RIKEN SPring-8 Center, Hyogo, Japan
| | | | - Yasuko Mori
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
- * E-mail:
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592
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Enhanced trimeric ACE2 exhibits potent prophylactic and therapeutic efficacy against the SARS-CoV-2 Delta and Omicron variants in vivo. Cell Res 2022; 32:589-592. [PMID: 35418217 PMCID: PMC9007249 DOI: 10.1038/s41422-022-00656-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 03/23/2022] [Indexed: 12/31/2022] Open
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593
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Kuzmina A, Wattad S, Engel S, Rosenberg E, Taube R. Functional Analysis of Spike from SARS-CoV-2 Variants Reveals the Role of Distinct Mutations in Neutralization Potential and Viral Infectivity. Viruses 2022; 14:v14040803. [PMID: 35458533 PMCID: PMC9030214 DOI: 10.3390/v14040803] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 04/04/2022] [Accepted: 04/07/2022] [Indexed: 12/11/2022] Open
Abstract
Enhanced viral transmission and escape from vaccine–elicited neutralizing antibodies drive worldwide spread of SARS-CoV-2 variants and promote disease progression. However, the impact of specific spike mutations that are carried by different viral variants on viral infectivity and neutralization sensitivity has not been completely defined. Here, we use pseudoviruses to assess the contribution of spike mutations within the Receptor Binding Domain (RBD) and the Furin Cleavage Site (FCS), and appear in circulating viral variants, on viral infectivity and neutralization potential against sera that was drawn from fully vaccinated individuals. Our functional analysis demonstrates that single, P681H, P681R or A701V–FCS mutations do not play a role in viral infectivity and neutralization potential. However, when in conjunction with the RBD–N501Y mutation, viral infectivity is enhanced. Similarly, combining the E484K–RBD mutation to the spike that carries FCS mutations reduces neutralization sensitivity with no effects on viral infectivity. Employing a similar approach onto the spike from Delta or Lota SARS-CoV-2 variants further reveals that specific RBD mutations affect neutralization sensitivity or viral infectivity differently. Our results validate the efficacy of the Pfizer third dose vaccine against Delta and Lota SARS-CoV-2 variants, and outline the significance of distinct RBD mutations in promoting viral infectivity and neutralization sensitivity to post–vaccination sera.
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Affiliation(s)
- Alona Kuzmina
- The Shraga Segal Department of Microbiology Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel; (A.K.); (S.W.)
| | - Seraj Wattad
- The Shraga Segal Department of Microbiology Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel; (A.K.); (S.W.)
| | - Stanislav Engel
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel;
| | | | - Ran Taube
- The Shraga Segal Department of Microbiology Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel; (A.K.); (S.W.)
- Correspondence:
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594
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The Importance of Vaccination in the Context of the COVID-19 Pandemic: A Brief Update Regarding the Use of Vaccines. Vaccines (Basel) 2022; 10:vaccines10040591. [PMID: 35455340 PMCID: PMC9027942 DOI: 10.3390/vaccines10040591] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/06/2022] [Accepted: 04/08/2022] [Indexed: 02/06/2023] Open
Abstract
The COVID-19 pandemic has led the world to undertake the largest vaccination campaign in human history. In record time, unprecedented scientific and governmental efforts have resulted in the acquisition of immunizers utilizing different technologies (nucleotide acids, viral vectors, inactivated and protein-based vaccines). Currently, 33 vaccines have already been approved by regulatory agencies in different countries, and more than 10 billion doses have been administered worldwide. Despite the undeniable impact of vaccination on the control of the pandemic, the recurrent emergence of new variants of interest has raised new challenges. The recent viral mutations precede new outbreaks that rapidly spread at global proportions. In addition, reducing protective efficacy rates have been observed among the main authorized vaccines. Besides these issues, several other crucial issues for the appropriate combatting of the pandemic remain uncertain or under investigation. Particularly noteworthy issues include the use of vaccine-boosting strategies to increase protection; concerns related to the long-term safety of vaccines, child immunization reliability and uncommon adverse events; the persistence of the virus in society; and the transition from a pandemic to an endemic state. In this review, we describe the updated scenario regarding SARS-CoV-2 variants and COVID-19 vaccines. In addition, we outline current discussions covering COVID-19 vaccine safety and efficacy, and the future pandemic perspectives.
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595
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Curlin ME, Bates TA, Guzman G, Schoen D, McBride SK, Carpenter SD, Tafesse FG. Omicron neutralizing antibody response following booster vaccination compared with breakthrough infection. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022. [PMID: 35441177 PMCID: PMC9016649 DOI: 10.1101/2022.04.11.22273694] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The rapid spread of the vaccine-resistant Omicron variant of SARS-CoV-2 presents a renewed threat to both unvaccinated and fully vaccinated individuals, and accelerated booster vaccination campaigns are underway to mitigate the ongoing wave of Omicron cases. The degree of immunity provided by standard vaccine regimens, boosted regimens, and immune responses elicited by the combination of vaccination and natural infection remain incompletely understood. The relative magnitude, quality and durability of serological responses, and the likelihood of neutralizing protection against future SARS-CoV-2 variants following these modes of exposure are unknown but are critical to the future trajectory of the COVID-19 pandemic. In this study of 99 vaccinated adults, we find that compared with responses after two doses of an mRNA regimen, the immune responses three months after a third vaccine dose and one month after breakthrough infection due to prior variants show dramatic increases in magnitude, potency, and breadth, including increased antibody dependent cellular phagocytosis and robust neutralization of the recently circulating Omicron variant. These results suggest that as the number of Omicron cases rise and as global vaccination and booster campaigns continue, an increasing proportion of the world’s population will acquire potent immune responses that may be protective against future SARS-CoV-2 variants.
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596
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Lee HK, Knabl L, Walter M, Furth PA, Hennighausen L. Limited cross-variant immune response from SARS-CoV-2 Omicron BA.2 in naïve but not previously infected outpatients.. [PMID: 35441161 PMCID: PMC9016656 DOI: 10.1101/2022.04.07.22273565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Omicron is currently the dominant SARS-CoV-2 variant and several sublineages have emerged. Questions remain about the impact of previous SARS-CoV-2 exposure on cross-variant immune responses elicited by BA.2 infection compared to BA.1. Here we show that without previous history of COVID-19, BA.2 infection induces a reduced immune response against all variants of concern (VOC) compared to BA.1 infection. The absence of ACE2 binding in sera of previously naïve BA.1 and BA.2 patients indicates a lack of meaningful neutralization. In contrast, anti-spike antibody levels and neutralizing activity greatly increased in the BA.1 and BA.2 patients with a previous history of COVID-19. Transcriptome analyses of peripheral immune cells showed significant differences in immune response and specific antibody generation between BA.1 and BA.2 patients as well as significant differences in expression of specific immune genes. In summary, prior infection status significantly impacts the innate and adaptive immune response against VOC following BA.2 infection.
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597
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Barre A, Klonjkowski B, Benoist H, Rougé P. How Do Point Mutations Enhancing the Basic Character of the RBDs of SARS-CoV-2 Variants Affect Their Transmissibility and Infectivity Capacities? Viruses 2022; 14:783. [PMID: 35458513 PMCID: PMC9031512 DOI: 10.3390/v14040783] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/03/2022] [Accepted: 04/08/2022] [Indexed: 11/30/2022] Open
Abstract
The spread of SARS-CoV-2 variants in the population depends on their ability to anchor the ACE2 receptor in the host cells. Differences in the electrostatic potentials of the spike protein RBD (electropositive/basic) and ACE2 receptor (electronegative/acidic) play a key role in both the rapprochement and the recognition of the coronavirus by the cell receptors. Accordingly, point mutations that result in an increase in electropositively charged residues, e.g., arginine and lysine, especially in the RBD of spike proteins in the SARS-CoV-2 variants, could contribute to their spreading capacity by favoring their recognition by the electronegatively charged ACE2 receptors. All SARS-CoV-2 variants that have been recognized as being highly transmissible, such as the kappa (κ), delta (δ) and omicron (o) variants, which display an enhanced electropositive character in their RBDs associated with a higher number of lysine- or arginine-generating point mutations. Lysine and arginine residues also participate in the enhanced RBD-ACE2 binding affinity of the omicron variant, by creating additional salt bridges with aspartic and glutamic acid residues from ACE2. However, the effects of lysine- and arginine-generating point mutations on infectivity is more contrasted, since the overall binding affinity of omicron RBD for ACE2 apparently results from some epistasis among the whole set of point mutations.
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Affiliation(s)
- Annick Barre
- UMR 152 PharmaDev, Faculté de Pharmacie, Institut de Recherche et Développement, Université Paul Sabatier, 35 Chemin des Maraîchers, 31062 Toulouse, France; (A.B.); (H.B.)
| | - Bernard Klonjkowski
- UMR Virologie, INRA, ANSES, Ecole Nationale Vétérinaire d’Alfort, 94700 Maisons-Alfort, France;
| | - Hervé Benoist
- UMR 152 PharmaDev, Faculté de Pharmacie, Institut de Recherche et Développement, Université Paul Sabatier, 35 Chemin des Maraîchers, 31062 Toulouse, France; (A.B.); (H.B.)
| | - Pierre Rougé
- UMR 152 PharmaDev, Faculté de Pharmacie, Institut de Recherche et Développement, Université Paul Sabatier, 35 Chemin des Maraîchers, 31062 Toulouse, France; (A.B.); (H.B.)
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598
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Tang H, Gao L, Wu Z, Meng F, Zhao X, Shao Y, Hou G, Du X, Qin FXF. Multiple SARS-CoV-2 Variants Exhibit Variable Target Cell Infectivity and Ability to Evade Antibody Neutralization. Front Immunol 2022; 13:836232. [PMID: 35371108 PMCID: PMC8966392 DOI: 10.3389/fimmu.2022.836232] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/15/2022] [Indexed: 01/21/2023] Open
Abstract
The continuous emergence of SARS-coronavirus 2 (SARS-CoV-2) variants, especially the variants of concern (VOC), exacerbated the impact of the coronavirus disease 2019 (COVID-19) pandemic. As the key of viral entry into host cells, the spike (S) protein is the major target of therapeutic monoclonal antibodies (mAbs) and polyclonal antibodies elicited by infection or vaccination. However, the mutations of S protein in variants may change the infectivity and antigenicity of SARS-CoV-2, leading to the immune escape from those neutralizing antibodies. To characterize the mutations of S protein in newly emerging variants, the proteolytic property and binding affinity with receptor were assessed, and the vesicular stomatitis virus (VSV)-based pseudovirus system was used to assess the infectivity and immune escape. We found that some SARS-CoV-2 variants have changed significantly in viral infectivity; especially, B.1.617.2 is more likely to infect less susceptible cells than D614G, and the virus infection process can be completed in a shorter time. In addition, neutralizing mAbs and vaccinated sera partially or completely failed to inhibit host cell entry mediated by the S protein of certain SARS-CoV-2 variants. However, SARS-CoV-2 variant S protein-mediated viral infection can still be blocked by protease inhibitors and endocytosis inhibitors. This work provides a deeper understanding of the rise and evolution of SARS-CoV-2 variants and their immune evasion.
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Affiliation(s)
- Haijun Tang
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Suzhou Institute of Systems Medicine, Suzhou, China
| | - Long Gao
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Suzhou Institute of Systems Medicine, Suzhou, China
| | - Zhao Wu
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Suzhou Institute of Systems Medicine, Suzhou, China
| | - Fang Meng
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Suzhou Institute of Systems Medicine, Suzhou, China
| | - Xin Zhao
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Suzhou Institute of Systems Medicine, Suzhou, China
| | - Yun Shao
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Suzhou Institute of Systems Medicine, Suzhou, China
| | - Guocun Hou
- Department of Nephrology, Suzhou Science and Technology Town Hospital, Suzhou, China
| | - Xiaohong Du
- Institute of Clinical Medicine Research, Suzhou Science and Technology Town Hospital, Suzhou, China
| | - F Xiao-Feng Qin
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Suzhou Institute of Systems Medicine, Suzhou, China
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599
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Sokal A, Broketa M, Barba-Spaeth G, Meola A, Fernández I, Fourati S, Azzaoui I, de La Selle A, Vandenberghe A, Roeser A, Bouvier-Alias M, Crickx E, Languille L, Michel M, Godeau B, Gallien S, Melica G, Nguyen Y, Zarrouk V, Canoui-Poitrine F, Noizat-Pirenne F, Megret J, Pawlotsky JM, Fillatreau S, Simon-Lorière E, Weill JC, Reynaud CA, Rey FA, Bruhns P, Chappert P, Mahévas M. Analysis of mRNA vaccination-elicited RBD-specific memory B cells reveals strong but incomplete immune escape of the SARS-CoV-2 Omicron variant. Immunity 2022; 55:1096-1104.e4. [PMID: 35483354 PMCID: PMC8986479 DOI: 10.1016/j.immuni.2022.04.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/16/2022] [Accepted: 04/04/2022] [Indexed: 11/05/2022]
Abstract
The SARS-CoV-2 Omicron variant can escape neutralization by vaccine-elicited and convalescent antibodies. Memory B cells (MBCs) represent another layer of protection against SARS-CoV-2, as they persist after infection and vaccination and improve their affinity. Whether MBCs elicited by mRNA vaccines can recognize the Omicron variant remains unclear. We assessed the affinity and neutralization potency against the Omicron variant of several hundred naturally expressed MBC-derived monoclonal IgG antibodies from vaccinated COVID-19-recovered and -naive individuals. Compared with other variants of concern, Omicron evaded recognition by a larger proportion of MBC-derived antibodies, with only 30% retaining high affinity against the Omicron RBD, and the reduction in neutralization potency was even more pronounced. Nonetheless, neutralizing MBC clones could be found in all the analyzed individuals. Therefore, despite the strong immune escape potential of the Omicron variant, these results suggest that the MBC repertoire generated by mRNA vaccines still provides some protection against the Omicron variant in vaccinated individuals.
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600
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Obireddy SR, Guntakanti U, Kowthalam A, Marata Chinna Subbarao S, Lai WF. Omicron: Understanding the latest variant of SARS-CoV-2 and strategies for tackling the infection. Chembiochem 2022; 23:e202200126. [PMID: 35362644 PMCID: PMC9083820 DOI: 10.1002/cbic.202200126] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 03/31/2022] [Indexed: 11/24/2022]
Abstract
The new variant of concern of SARS‐CoV‐2, namely Omicron, has triggered global fear recently. To date, our knowledge of Omicron, particularly of how S glycoprotein mutations affect the infectivity of the virus and the severity of the infection, is far from complete. This hinders our ability to treat the disease and to predict the future state of SARS‐CoV‐2 threats to well‐being and economic stability. Despite this, efforts have been made to unveil the routes of transmission and the efficiency of existing vaccines in tackling Omicron. This article reviews the latest understanding of Omicron and the current status of the use of vaccines and drugs for infection control. It is hoped that this article can offer insights into the development of more effective measures to tackle the pandemic.
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Affiliation(s)
- Sreekanth Reddy Obireddy
- Sri Krishnadevaraya University, Chemistry, TIRUPATI NATIONAL HIGHWAY, ITUKALAPALLI, 515004, India, 515003, ANANTHAPURAMU, INDIA
| | | | | | | | - Wing-Fu Lai
- The Chinese University of Hong Kong, School of Life and Health Sciences, 518172, Shenzhen, CHINA
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